rs7042485

Variant names:

• chr9-113385961-G-A
• rs7042485

Your query was ambiguous. Multiple possible variants found:

• chr9-113385961-G-A
• chr9-113385961-G-C

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 0.672 in 152,078 control chromosomes in the GnomAD database, including 34,681 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 0.67 (34681 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.99
• Publications: 4 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 (AFR) allele frequency at 95% confidence interval = 0.694 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: 0.672 AC: 102158 AN: 151960 Hom.: 34646 Cov.: 32

Gnomad AFR AF: 0.701

Gnomad AMI AF: 0.484

Gnomad AMR AF: 0.581

Gnomad ASJ AF: 0.674

Gnomad EAS AF: 0.478

Gnomad SAS AF: 0.602

Gnomad FIN AF: 0.745

Gnomad MID AF: 0.630

Gnomad NFE AF: 0.687

Gnomad OTH AF: 0.666

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

GnomAD4 genome AF: 0.672 AC: 102249 AN: 152078 Hom.: 34681 Cov.: 32 AF XY: 0.671 AC XY: 49838 AN XY: 74328

African (AFR) AF: 0.701 AC: 29100 AN: 41498

American (AMR) AF: 0.580 AC: 8860 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.674 AC: 2341 AN: 3472

East Asian (EAS) AF: 0.478 AC: 2463 AN: 5158

South Asian (SAS) AF: 0.602 AC: 2896 AN: 4814

European-Finnish (FIN) AF: 0.745 AC: 7874 AN: 10576

Middle Eastern (MID) AF: 0.626 AC: 184 AN: 294

European-Non Finnish (NFE) AF: 0.687 AC: 46683 AN: 67984

Other (OTH) AF: 0.669 AC: 1411 AN: 2110

Alfa AF: 0.675 Hom.: 73237

Bravo AF: 0.656

Asia WGS AF: 0.580 AC: 2016 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	7.0
DANN	Benign	0.76
PhyloP100		2.0

Splicing

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

Other links and lift over

dbSNP: rs7042485; hg19: chr9-116148241; COSMIC: COSV52958355;