rs9461607

Variant names:

• chr6-30446797-C-A
• rs9461607

Your query was ambiguous. Multiple possible variants found:

• chr6-30446797-C-A
• chr6-30446797-C-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 0.164 in 152,092 control chromosomes in the GnomAD database, including 2,227 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 0.16 (2227 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.458
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.237 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: 0.164 AC: 24875 AN: 151974 Hom.: 2227 Cov.: 32

Gnomad AFR AF: 0.242

Gnomad AMI AF: 0.147

Gnomad AMR AF: 0.107

Gnomad ASJ AF: 0.134

Gnomad EAS AF: 0.0312

Gnomad SAS AF: 0.139

Gnomad FIN AF: 0.0889

Gnomad MID AF: 0.108

Gnomad NFE AF: 0.155

Gnomad OTH AF: 0.154

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

GnomAD4 genome AF: 0.164 AC: 24890 AN: 152092 Hom.: 2227 Cov.: 32 AF XY: 0.159 AC XY: 11799 AN XY: 74358

African (AFR) AF: 0.241 AC: 10003 AN: 41430

American (AMR) AF: 0.106 AC: 1626 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.134 AC: 464 AN: 3464

East Asian (EAS) AF: 0.0314 AC: 163 AN: 5186

South Asian (SAS) AF: 0.140 AC: 677 AN: 4826

European-Finnish (FIN) AF: 0.0889 AC: 942 AN: 10592

Middle Eastern (MID) AF: 0.0952 AC: 28 AN: 294

European-Non Finnish (NFE) AF: 0.155 AC: 10532 AN: 68000

Other (OTH) AF: 0.152 AC: 321 AN: 2106

Alfa AF: 0.0770 Hom.: 116

Bravo AF: 0.172

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.5
DANN	Benign	0.23
PhyloP100		-0.46

Splicing

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

Other links and lift over

dbSNP: rs9461607; hg19: chr6-30414574;