17-40287379-A-G

Variant names:

• chr17-40287379-A-G
• rs4134994

Variant summary

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

The variant allele was found at a frequency of 0.239 in 152,032 control chromosomes in the GnomAD database, including 6,228 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.24 (6228 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -1.55
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BP6: Variant 17-40287379-A-G is Benign according to our data. Variant chr17-40287379-A-G is described in ClinVar as Benign. ClinVar VariationId is 1169222.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.481 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.239 AC: 36236 AN: 151912 Hom.: 6190 Cov.: 32

Gnomad AFR AF: 0.486

Gnomad AMI AF: 0.208

Gnomad AMR AF: 0.172

Gnomad ASJ AF: 0.0953

Gnomad EAS AF: 0.349

Gnomad SAS AF: 0.109

Gnomad FIN AF: 0.144

Gnomad MID AF: 0.127

Gnomad NFE AF: 0.128

Gnomad OTH AF: 0.194

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

GnomAD4 genome AF: 0.239 AC: 36334 AN: 152032 Hom.: 6228 Cov.: 32 AF XY: 0.238 AC XY: 17692 AN XY: 74328

African (AFR) AF: 0.486 AC: 20141 AN: 41402

American (AMR) AF: 0.173 AC: 2638 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.0953 AC: 331 AN: 3472

East Asian (EAS) AF: 0.349 AC: 1801 AN: 5166

South Asian (SAS) AF: 0.110 AC: 531 AN: 4824

European-Finnish (FIN) AF: 0.144 AC: 1521 AN: 10584

Middle Eastern (MID) AF: 0.136 AC: 40 AN: 294

European-Non Finnish (NFE) AF: 0.128 AC: 8732 AN: 67982

Other (OTH) AF: 0.194 AC: 409 AN: 2110

Alfa AF: 0.211 Hom.: 2371

Bravo AF: 0.254

Asia WGS AF: 0.237 AC: 825 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Jan 13, 2025

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	0.68
DANN	Benign	0.35
PhyloP100		-1.5
PromoterAI		0.025	Neutral

Splicing

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

Other links and lift over

dbSNP: rs4134994; hg19: chr17-38443631;