rs4897081

Variant names:

• chr6-149115402-G-A
• rs4897081

Your query was ambiguous. Multiple possible variants found:

• chr6-149115402-G-A
• chr6-149115402-G-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 0.414 in 151,954 control chromosomes in the GnomAD database, including 13,464 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 0.41 (13464 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.109

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.517 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: 0.413 AC: 62755 AN: 151836 Hom.: 13437 Cov.: 31

Gnomad AFR AF: 0.522

Gnomad AMI AF: 0.269

Gnomad AMR AF: 0.395

Gnomad ASJ AF: 0.491

Gnomad EAS AF: 0.283

Gnomad SAS AF: 0.391

Gnomad FIN AF: 0.394

Gnomad MID AF: 0.389

Gnomad NFE AF: 0.363

Gnomad OTH AF: 0.441

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

GnomAD4 genome AF: 0.414 AC: 62844 AN: 151954 Hom.: 13464 Cov.: 31 AF XY: 0.415 AC XY: 30809 AN XY: 74272

Gnomad4 AFR AF: 0.523

Gnomad4 AMR AF: 0.394

Gnomad4 ASJ AF: 0.491

Gnomad4 EAS AF: 0.283

Gnomad4 SAS AF: 0.391

Gnomad4 FIN AF: 0.394

Gnomad4 NFE AF: 0.363

Gnomad4 OTH AF: 0.441

Alfa AF: 0.381 Hom.: 18066

Bravo AF: 0.420

Asia WGS AF: 0.406 AC: 1408 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	3.1
DANN	Benign	0.65

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4897081; hg19: chr6-149436538;