rs7042485

chr9-113385961-G-Achr9-113385961-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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;