rs4897081

Positions:

• 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/exons	MANE	UniProt

Ensembl

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