rs7862042

Variant names:

• chr9-5268139-G-A
• rs7862042

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 0.332 in 151,964 control chromosomes in the GnomAD database, including 8,902 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 0.33 (8902 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.902
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.447 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: 0.332 AC: 50425 AN: 151846 Hom.: 8898 Cov.: 32

Gnomad AFR AF: 0.452

Gnomad AMI AF: 0.309

Gnomad AMR AF: 0.301

Gnomad ASJ AF: 0.253

Gnomad EAS AF: 0.231

Gnomad SAS AF: 0.305

Gnomad FIN AF: 0.353

Gnomad MID AF: 0.196

Gnomad NFE AF: 0.278

Gnomad OTH AF: 0.301

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

GnomAD4 genome AF: 0.332 AC: 50464 AN: 151964 Hom.: 8902 Cov.: 32 AF XY: 0.333 AC XY: 24697 AN XY: 74270

African (AFR) AF: 0.452 AC: 18721 AN: 41424

American (AMR) AF: 0.301 AC: 4591 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.253 AC: 877 AN: 3470

East Asian (EAS) AF: 0.231 AC: 1189 AN: 5158

South Asian (SAS) AF: 0.305 AC: 1473 AN: 4824

European-Finnish (FIN) AF: 0.353 AC: 3728 AN: 10552

Middle Eastern (MID) AF: 0.180 AC: 53 AN: 294

European-Non Finnish (NFE) AF: 0.278 AC: 18921 AN: 67950

Other (OTH) AF: 0.298 AC: 630 AN: 2114

Alfa AF: 0.296 Hom.: 3494

Bravo AF: 0.329

Asia WGS AF: 0.262 AC: 909 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.72
DANN	Benign	0.57
PhyloP100		-0.90

Splicing

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

Other links and lift over

dbSNP: rs7862042; hg19: chr9-5268139; COSMIC: COSV60323936;