rs4897336

Variant names:

• chr6-129760916-G-A
• rs4897336

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 0.135 in 152,132 control chromosomes in the GnomAD database, including 2,031 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 0.13 (2031 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.25

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.49 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: 0.135 AC: 20480 AN: 152014 Hom.: 2026 Cov.: 32

Gnomad AFR AF: 0.154

Gnomad AMI AF: 0.0461

Gnomad AMR AF: 0.206

Gnomad ASJ AF: 0.141

Gnomad EAS AF: 0.506

Gnomad SAS AF: 0.171

Gnomad FIN AF: 0.0923

Gnomad MID AF: 0.155

Gnomad NFE AF: 0.0837

Gnomad OTH AF: 0.136

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

GnomAD4 genome AF: 0.135 AC: 20503 AN: 152132 Hom.: 2031 Cov.: 32 AF XY: 0.138 AC XY: 10284 AN XY: 74360

Gnomad4 AFR AF: 0.154

Gnomad4 AMR AF: 0.207

Gnomad4 ASJ AF: 0.141

Gnomad4 EAS AF: 0.506

Gnomad4 SAS AF: 0.169

Gnomad4 FIN AF: 0.0923

Gnomad4 NFE AF: 0.0837

Gnomad4 OTH AF: 0.136

Alfa AF: 0.101 Hom.: 2055

Bravo AF: 0.148

Asia WGS AF: 0.334 AC: 1159 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	5.9
DANN	Benign	0.42

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4897336; hg19: chr6-130082061;