9-134441602-A-G

Variant names:

• chr9-134441602-A-G
• rs4842198

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 0.642 in 150,408 control chromosomes in the GnomAD database, including 33,724 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 0.64 (33724 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.294
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.781 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: 0.643 AC: 96615 AN: 150304 Hom.: 33734 Cov.: 31

Gnomad AFR AF: 0.347

Gnomad AMI AF: 0.691

Gnomad AMR AF: 0.651

Gnomad ASJ AF: 0.779

Gnomad EAS AF: 0.664

Gnomad SAS AF: 0.540

Gnomad FIN AF: 0.820

Gnomad MID AF: 0.690

Gnomad NFE AF: 0.787

Gnomad OTH AF: 0.653

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

GnomAD4 genome AF: 0.642 AC: 96610 AN: 150408 Hom.: 33724 Cov.: 31 AF XY: 0.645 AC XY: 47371 AN XY: 73492

African (AFR) AF: 0.347 AC: 14004 AN: 40410

American (AMR) AF: 0.650 AC: 9879 AN: 15188

Ashkenazi Jewish (ASJ) AF: 0.779 AC: 2700 AN: 3464

East Asian (EAS) AF: 0.664 AC: 3380 AN: 5092

South Asian (SAS) AF: 0.540 AC: 2562 AN: 4748

European-Finnish (FIN) AF: 0.820 AC: 8619 AN: 10510

Middle Eastern (MID) AF: 0.680 AC: 200 AN: 294

European-Non Finnish (NFE) AF: 0.787 AC: 53287 AN: 67702

Other (OTH) AF: 0.646 AC: 1353 AN: 2094

Alfa AF: 0.582 Hom.: 10382

Bravo AF: 0.617

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.16
DANN	Benign	0.24
PhyloP100		-0.29

Splicing

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

Other links and lift over

dbSNP: rs4842198; hg19: chr9-137333448; COSMIC: COSV62683932;