rs2011732

Variant names:

• chr17-63919139-C-A
• rs2011732
• ENST00000647774.1:c.287-633G>T

Variant summary

Our verdict is Benign. The variant received -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The ENST00000647774.1(ENSG00000285947):​c.287-633G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.219 in 152,124 control chromosomes in the GnomAD database, including 3,759 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.22 (3759 hom., cov: 32)
• Consequence: ENSG00000285947 ENST00000647774.1 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.278
• Publications: 6 publications found

Genes affected

ENSG00000285947 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BP6: Variant 17-63919139-C-A is Benign according to our data. Variant chr17-63919139-C-A is described in ClinVar as Benign. ClinVar VariationId is 1296769.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.242 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000647774.1. 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
	ENSG00000285947	ENST00000647774.1		c.287-633G>T		intron	N/A	ENSP00000497443.1

Frequencies

GnomAD3 genomes AF: 0.219 AC: 33245 AN: 152008 Hom.: 3760 Cov.: 32

Gnomad AFR AF: 0.234

Gnomad AMI AF: 0.286

Gnomad AMR AF: 0.158

Gnomad ASJ AF: 0.180

Gnomad EAS AF: 0.0570

Gnomad SAS AF: 0.149

Gnomad FIN AF: 0.189

Gnomad MID AF: 0.332

Gnomad NFE AF: 0.245

Gnomad OTH AF: 0.229

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

GnomAD4 genome AF: 0.219 AC: 33240 AN: 152124 Hom.: 3759 Cov.: 32 AF XY: 0.213 AC XY: 15811 AN XY: 74364

African (AFR) AF: 0.234 AC: 9719 AN: 41490

American (AMR) AF: 0.158 AC: 2415 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.180 AC: 623 AN: 3468

East Asian (EAS) AF: 0.0569 AC: 295 AN: 5180

South Asian (SAS) AF: 0.148 AC: 712 AN: 4826

European-Finnish (FIN) AF: 0.189 AC: 1999 AN: 10586

Middle Eastern (MID) AF: 0.332 AC: 97 AN: 292

European-Non Finnish (NFE) AF: 0.245 AC: 16642 AN: 67966

Other (OTH) AF: 0.227 AC: 478 AN: 2110

Alfa AF: 0.229 Hom.: 485

Bravo AF: 0.216

ClinVar

ClinVar submissions as Germline

Significance: Benign

Revision: criteria provided, single submitter

Pathogenic	VUS	Benign	Condition
-	-	1	not provided (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	1.2
DANN	Benign	0.82
PhyloP100		-0.28
PromoterAI		0.061	Neutral

Splicing

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

Other links and lift over

dbSNP: rs2011732; hg19: chr17-61996499;