9-4972398-C-T

Variant names:

• chr9-4972398-C-T
• rs7862852

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 0.664 in 151,522 control chromosomes in the GnomAD database, including 33,495 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 0.66 (33495 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.145
• Publications: 10 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.701 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: 0.664 AC: 100543 AN: 151402 Hom.: 33464 Cov.: 32

Gnomad AFR AF: 0.708

Gnomad AMI AF: 0.654

Gnomad AMR AF: 0.679

Gnomad ASJ AF: 0.733

Gnomad EAS AF: 0.649

Gnomad SAS AF: 0.661

Gnomad FIN AF: 0.673

Gnomad MID AF: 0.608

Gnomad NFE AF: 0.630

Gnomad OTH AF: 0.673

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

GnomAD4 genome AF: 0.664 AC: 100626 AN: 151522 Hom.: 33495 Cov.: 32 AF XY: 0.665 AC XY: 49207 AN XY: 74018

African (AFR) AF: 0.708 AC: 29230 AN: 41268

American (AMR) AF: 0.679 AC: 10361 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.733 AC: 2538 AN: 3462

East Asian (EAS) AF: 0.649 AC: 3336 AN: 5142

South Asian (SAS) AF: 0.661 AC: 3181 AN: 4814

European-Finnish (FIN) AF: 0.673 AC: 7064 AN: 10500

Middle Eastern (MID) AF: 0.588 AC: 173 AN: 294

European-Non Finnish (NFE) AF: 0.630 AC: 42737 AN: 67790

Other (OTH) AF: 0.675 AC: 1419 AN: 2102

Alfa AF: 0.649 Hom.: 100022

Bravo AF: 0.666

Asia WGS AF: 0.707 AC: 2456 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.84
DANN	Benign	0.45
PhyloP100		-0.14

Splicing

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

Other links and lift over

dbSNP: rs7862852; hg19: chr9-4972398; COSMIC: COSV71837668;