rs4134994

chr17-40287379-A-Gchr17-40287379-A-T

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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 id 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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	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

Gnomad4 AFR AF: 0.486

Gnomad4 AMR AF: 0.173

Gnomad4 ASJ AF: 0.0953

Gnomad4 EAS AF: 0.349

Gnomad4 SAS AF: 0.110

Gnomad4 FIN AF: 0.144

Gnomad4 NFE AF: 0.128

Gnomad4 OTH AF: 0.194

Alfa AF: 0.127 Hom.: 582

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

Benign, criteria provided, single submitter

clinical testing

Invitae

Jan 08, 2024

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
Cadd	Benign	0.68
Dann	Benign	0.35

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4134994; hg19: chr17-38443631;