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. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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

Gnomad4 AFR AF: 0.701

Gnomad4 AMR AF: 0.580

Gnomad4 ASJ AF: 0.674

Gnomad4 EAS AF: 0.478

Gnomad4 SAS AF: 0.602

Gnomad4 FIN AF: 0.745

Gnomad4 NFE AF: 0.687

Gnomad4 OTH AF: 0.669

Alfa AF: 0.677 Hom.: 19439

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

Splicing

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

Publications

LitVar

Other links and lift over

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