rs4842196

chr9-134441382-C-Achr9-134441382-C-Gchr9-134441382-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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;