rs4610597

Variant names:

• chr6-103776002-G-A
• rs4610597

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 0.0844 in 151,990 control chromosomes in the GnomAD database, including 978 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 0.084 (978 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.556
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.205 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: 0.0844 AC: 12818 AN: 151870 Hom.: 976 Cov.: 32

Gnomad AFR AF: 0.209

Gnomad AMI AF: 0.0428

Gnomad AMR AF: 0.0577

Gnomad ASJ AF: 0.0930

Gnomad EAS AF: 0.000967

Gnomad SAS AF: 0.0186

Gnomad FIN AF: 0.0212

Gnomad MID AF: 0.120

Gnomad NFE AF: 0.0360

Gnomad OTH AF: 0.0722

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

GnomAD4 genome AF: 0.0844 AC: 12835 AN: 151990 Hom.: 978 Cov.: 32 AF XY: 0.0819 AC XY: 6084 AN XY: 74310

African (AFR) AF: 0.209 AC: 8646 AN: 41414

American (AMR) AF: 0.0575 AC: 876 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.0930 AC: 322 AN: 3464

East Asian (EAS) AF: 0.000969 AC: 5 AN: 5160

South Asian (SAS) AF: 0.0186 AC: 90 AN: 4828

European-Finnish (FIN) AF: 0.0212 AC: 225 AN: 10594

Middle Eastern (MID) AF: 0.116 AC: 34 AN: 294

European-Non Finnish (NFE) AF: 0.0360 AC: 2448 AN: 67962

Other (OTH) AF: 0.0710 AC: 150 AN: 2114

Alfa AF: 0.0502 Hom.: 565

Bravo AF: 0.0936

Asia WGS AF: 0.0230 AC: 82 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	1.0
DANN	Benign	0.22
PhyloP100		-0.56

Splicing

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

Other links and lift over

dbSNP: rs4610597; hg19: chr6-104223877;