rs4842196

Variant names:

• chr9-134441382-C-A
• rs4842196

Your query was ambiguous. Multiple possible variants found:

• chr9-134441382-C-A
• chr9-134441382-C-G
• chr9-134441382-C-T

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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

Gnomad4 AFR AF: 0.335

Gnomad4 AMR AF: 0.634

Gnomad4 ASJ AF: 0.747

Gnomad4 EAS AF: 0.660

Gnomad4 SAS AF: 0.523

Gnomad4 FIN AF: 0.737

Gnomad4 NFE AF: 0.750

Gnomad4 OTH AF: 0.632

Alfa AF: 0.693 Hom.: 20060

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

Splicing

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

Publications

LitVar

Other links and lift over

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