rs7863238

Variant names:

• chr9-73082248-T-C
• rs7863238

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 0.564 in 152,002 control chromosomes in the GnomAD database, including 24,643 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 0.56 (24643 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.14
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.606 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.564 AC: 85618 AN: 151882 Hom.: 24623 Cov.: 31

Gnomad AFR AF: 0.465

Gnomad AMI AF: 0.631

Gnomad AMR AF: 0.603

Gnomad ASJ AF: 0.508

Gnomad EAS AF: 0.414

Gnomad SAS AF: 0.541

Gnomad FIN AF: 0.685

Gnomad MID AF: 0.554

Gnomad NFE AF: 0.610

Gnomad OTH AF: 0.580

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

GnomAD4 genome AF: 0.564 AC: 85686 AN: 152002 Hom.: 24643 Cov.: 31 AF XY: 0.567 AC XY: 42128 AN XY: 74278

African (AFR) AF: 0.465 AC: 19276 AN: 41426

American (AMR) AF: 0.603 AC: 9210 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.508 AC: 1763 AN: 3472

East Asian (EAS) AF: 0.414 AC: 2134 AN: 5156

South Asian (SAS) AF: 0.543 AC: 2619 AN: 4824

European-Finnish (FIN) AF: 0.685 AC: 7243 AN: 10570

Middle Eastern (MID) AF: 0.551 AC: 162 AN: 294

European-Non Finnish (NFE) AF: 0.610 AC: 41487 AN: 67962

Other (OTH) AF: 0.577 AC: 1218 AN: 2110

Alfa AF: 0.590 Hom.: 13590

Bravo AF: 0.552

Asia WGS AF: 0.476 AC: 1660 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.28
DANN	Benign	0.77
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs7863238; hg19: chr9-75697164;