chr9-134441382-C-A

Variant names:

• chr9-134441382-C-A
• rs4842196

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 0.612 in 152,066 control chromosomes in the GnomAD database, including 30,983 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 0.61 (30983 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.671
• Publications: 12 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 = 0.744 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: 0.613 AC: 93087 AN: 151948 Hom.: 30995 Cov.: 33

Gnomad AFR AF: 0.336

Gnomad AMI AF: 0.764

Gnomad AMR AF: 0.634

Gnomad ASJ AF: 0.747

Gnomad EAS AF: 0.661

Gnomad SAS AF: 0.524

Gnomad FIN AF: 0.737

Gnomad MID AF: 0.696

Gnomad NFE AF: 0.750

Gnomad OTH AF: 0.639

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

GnomAD4 genome AF: 0.612 AC: 93079 AN: 152066 Hom.: 30983 Cov.: 33 AF XY: 0.613 AC XY: 45524 AN XY: 74318

African (AFR) AF: 0.335 AC: 13904 AN: 41500

American (AMR) AF: 0.634 AC: 9687 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.747 AC: 2592 AN: 3470

East Asian (EAS) AF: 0.660 AC: 3400 AN: 5150

South Asian (SAS) AF: 0.523 AC: 2521 AN: 4822

European-Finnish (FIN) AF: 0.737 AC: 7788 AN: 10572

Middle Eastern (MID) AF: 0.690 AC: 203 AN: 294

European-Non Finnish (NFE) AF: 0.750 AC: 50953 AN: 67950

Other (OTH) AF: 0.632 AC: 1334 AN: 2112

Alfa AF: 0.690 Hom.: 33366

Bravo AF: 0.598

Asia WGS AF: 0.573 AC: 1993 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.1
DANN	Benign	0.49
PhyloP100		0.67

Splicing

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

Other links and lift over

dbSNP: rs4842196; hg19: chr9-137333228; COSMIC: COSV62683928;