17-70831948-C-A

Variant names:

• chr17-70831948-C-A
• rs1990193
• ENST00000774266.1:n.247-65724C>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000774266.1(ENSG00000300827):​n.247-65724C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.509 in 151,872 control chromosomes in the GnomAD database, including 19,944 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.51 (19944 hom., cov: 32)
• Consequence: ENSG00000300827 ENST00000774266.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.101
• Publications: 5 publications found

Genes affected

ENSG00000300827 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.728 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000774266.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000300827	ENST00000774266.1		n.247-65724C>A		intron	N/A
	ENSG00000300827	ENST00000774267.1		n.186-65724C>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.509 AC: 77229 AN: 151754 Hom.: 19930 Cov.: 32

Gnomad AFR AF: 0.490

Gnomad AMI AF: 0.593

Gnomad AMR AF: 0.587

Gnomad ASJ AF: 0.451

Gnomad EAS AF: 0.748

Gnomad SAS AF: 0.492

Gnomad FIN AF: 0.525

Gnomad MID AF: 0.494

Gnomad NFE AF: 0.486

Gnomad OTH AF: 0.500

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.509 AC: 77273 AN: 151872 Hom.: 19944 Cov.: 32 AF XY: 0.513 AC XY: 38082 AN XY: 74240

African (AFR) AF: 0.489 AC: 20257 AN: 41416

American (AMR) AF: 0.587 AC: 8949 AN: 15244

Ashkenazi Jewish (ASJ) AF: 0.451 AC: 1563 AN: 3466

East Asian (EAS) AF: 0.748 AC: 3860 AN: 5160

South Asian (SAS) AF: 0.493 AC: 2374 AN: 4812

European-Finnish (FIN) AF: 0.525 AC: 5536 AN: 10554

Middle Eastern (MID) AF: 0.497 AC: 145 AN: 292

European-Non Finnish (NFE) AF: 0.486 AC: 32996 AN: 67912

Other (OTH) AF: 0.500 AC: 1056 AN: 2110

Alfa AF: 0.497 Hom.: 56082

Bravo AF: 0.512

Asia WGS AF: 0.565 AC: 1962 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.5
DANN	Benign	0.27
PhyloP100		-0.10

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs1990193;

hg19: chr17-68828089;