17-9917378-C-T

Variant names:

• chr17-9917378-C-T
• rs4791910
• NM_201433.2:c.1318-37G>A

Variant summary

Our verdict is Benign. The variant received -20 ACMG points: 0P and 20B. BP4_Strong BP6_Very_Strong BA1

The NM_201433.2(GAS7):​c.1318-37G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.547 in 1,427,730 control chromosomes in the GnomAD database, including 217,186 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

• Frequency:
  • Genomes: 𝑓 0.52 (20843 hom., cov: 35)
  • Exomes 𝑓: 0.55 (196343 hom.)
• Consequence: GAS7 NM_201433.2 intron
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:2
• Conservation: PhyloP100: -0.495
• Publications: 15 publications found

Genes affected

GAS7 (HGNC:4169): (growth arrest specific 7) Growth arrest-specific 7 is expressed primarily in terminally differentiated brain cells and predominantly in mature cerebellar Purkinje neurons. GAS7 plays a putative role in neuronal development. Several transcript variants encoding proteins which vary in the N-terminus have been described. [provided by RefSeq, Jul 2008]

ACMG classification

Our verdict: Benign. The variant received -20 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BP6: Variant 17-9917378-C-T is Benign according to our data. Variant chr17-9917378-C-T is described in ClinVar as Benign. ClinVar VariationId is 1222796.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.563 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_201433.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GAS7	NM_201433.2	MANE Select	c.1318-37G>A		intron	N/A	NP_958839.1	O60861-3
	GAS7	NM_201432.2		c.1138-37G>A		intron	N/A	NP_958836.1	O60861-4
	GAS7	NM_001130831.2		c.1126-37G>A		intron	N/A	NP_001124303.1	O60861-1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GAS7	ENST00000432992.7	TSL:1 MANE Select	c.1318-37G>A		intron	N/A	ENSP00000407552.2	O60861-3
	GAS7	ENST00000323816.8	TSL:1	c.1138-37G>A		intron	N/A	ENSP00000322608.5	O60861-4
	GAS7	ENST00000585266.5	TSL:1	c.1138-37G>A		intron	N/A	ENSP00000464240.2	O60861-4

Frequencies

GnomAD3 genomes AF: 0.519 AC: 78978 AN: 152046 Hom.: 20835 Cov.: 35

Gnomad AFR AF: 0.449

Gnomad AMI AF: 0.481

Gnomad AMR AF: 0.488

Gnomad ASJ AF: 0.520

Gnomad EAS AF: 0.554

Gnomad SAS AF: 0.403

Gnomad FIN AF: 0.569

Gnomad MID AF: 0.522

Gnomad NFE AF: 0.568

Gnomad OTH AF: 0.516

GnomAD2 exomes AF: 0.526 AC: 130736 AN: 248758 AF XY: 0.521

Gnomad AFR exome AF: 0.451

Gnomad AMR exome AF: 0.492

Gnomad ASJ exome AF: 0.507

Gnomad EAS exome AF: 0.576

Gnomad FIN exome AF: 0.568

Gnomad NFE exome AF: 0.563

Gnomad OTH exome AF: 0.541

GnomAD4 exome AF: 0.551 AC: 702486 AN: 1275566 Hom.: 196343 Cov.: 19 AF XY: 0.546 AC XY: 351749 AN XY: 644410

African (AFR) AF: 0.436 AC: 13079 AN: 30020

American (AMR) AF: 0.493 AC: 21884 AN: 44382

Ashkenazi Jewish (ASJ) AF: 0.501 AC: 12514 AN: 24954

East Asian (EAS) AF: 0.559 AC: 21712 AN: 38866

South Asian (SAS) AF: 0.408 AC: 33715 AN: 82698

European-Finnish (FIN) AF: 0.559 AC: 29696 AN: 53162

Middle Eastern (MID) AF: 0.510 AC: 2779 AN: 5446

European-Non Finnish (NFE) AF: 0.571 AC: 538114 AN: 941918

Other (OTH) AF: 0.536 AC: 28993 AN: 54120

GnomAD4 genome AF: 0.519 AC: 79016 AN: 152164 Hom.: 20843 Cov.: 35 AF XY: 0.517 AC XY: 38434 AN XY: 74376

African (AFR) AF: 0.449 AC: 18640 AN: 41526

American (AMR) AF: 0.488 AC: 7474 AN: 15306

Ashkenazi Jewish (ASJ) AF: 0.520 AC: 1803 AN: 3468

East Asian (EAS) AF: 0.552 AC: 2854 AN: 5166

South Asian (SAS) AF: 0.402 AC: 1943 AN: 4828

European-Finnish (FIN) AF: 0.569 AC: 6022 AN: 10584

Middle Eastern (MID) AF: 0.514 AC: 151 AN: 294

European-Non Finnish (NFE) AF: 0.568 AC: 38608 AN: 67972

Other (OTH) AF: 0.513 AC: 1084 AN: 2112

Alfa AF: 0.550 Hom.: 97563

Bravo AF: 0.511

Asia WGS AF: 0.479 AC: 1666 AN: 3478

ClinVar

ClinVar submissions

Significance: Benign

Revision: criteria provided, multiple submitters, no conflicts

Pathogenic	VUS	Benign	Condition
-	-	2	not provided (2)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.062
DANN	Benign	0.66
PhyloP100		-0.49
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs4791910; hg19: chr17-9820695;