rs4796606

Variant names:

• chr17-41507835-G-A
• rs4796606

Your query was ambiguous. Multiple possible variants found:

• chr17-41507835-G-A
• chr17-41507835-G-T

Variant summary

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

The variant allele was found at a frequency of 0.875 in 152,220 control chromosomes in the GnomAD database, including 59,249 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 0.87 (59249 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.111
• Publications: 9 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.949 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.875 AC: 133069 AN: 152102 Hom.: 59227 Cov.: 32

Gnomad AFR AF: 0.694

Gnomad AMI AF: 0.948

Gnomad AMR AF: 0.916

Gnomad ASJ AF: 0.929

Gnomad EAS AF: 0.971

Gnomad SAS AF: 0.916

Gnomad FIN AF: 0.968

Gnomad MID AF: 0.842

Gnomad NFE AF: 0.947

Gnomad OTH AF: 0.875

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

GnomAD4 genome AF: 0.875 AC: 133138 AN: 152220 Hom.: 59249 Cov.: 32 AF XY: 0.877 AC XY: 65243 AN XY: 74428

African (AFR) AF: 0.694 AC: 28788 AN: 41476

American (AMR) AF: 0.916 AC: 14022 AN: 15306

Ashkenazi Jewish (ASJ) AF: 0.929 AC: 3222 AN: 3470

East Asian (EAS) AF: 0.971 AC: 5015 AN: 5164

South Asian (SAS) AF: 0.916 AC: 4423 AN: 4828

European-Finnish (FIN) AF: 0.968 AC: 10278 AN: 10622

Middle Eastern (MID) AF: 0.833 AC: 245 AN: 294

European-Non Finnish (NFE) AF: 0.947 AC: 64436 AN: 68036

Other (OTH) AF: 0.873 AC: 1844 AN: 2112

Alfa AF: 0.928 Hom.: 33262

Bravo AF: 0.862

Asia WGS AF: 0.908 AC: 3159 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	2.3
DANN	Benign	0.84
PhyloP100		-0.11

Splicing

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

Other links and lift over

dbSNP: rs4796606; hg19: chr17-39664087;