6-149441401-A-G

Variant names:

• chr6-149441401-A-G
• rs2179367

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 0.499 in 151,794 control chromosomes in the GnomAD database, including 20,647 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 0.50 (20647 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.78

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.731 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: 0.499 AC: 75645 AN: 151676 Hom.: 20602 Cov.: 30

Gnomad AFR AF: 0.691

Gnomad AMI AF: 0.233

Gnomad AMR AF: 0.547

Gnomad ASJ AF: 0.426

Gnomad EAS AF: 0.750

Gnomad SAS AF: 0.520

Gnomad FIN AF: 0.391

Gnomad MID AF: 0.430

Gnomad NFE AF: 0.375

Gnomad OTH AF: 0.497

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

GnomAD4 genome AF: 0.499 AC: 75745 AN: 151794 Hom.: 20647 Cov.: 30 AF XY: 0.502 AC XY: 37275 AN XY: 74188

Gnomad4 AFR AF: 0.691

Gnomad4 AMR AF: 0.548

Gnomad4 ASJ AF: 0.426

Gnomad4 EAS AF: 0.750

Gnomad4 SAS AF: 0.518

Gnomad4 FIN AF: 0.391

Gnomad4 NFE AF: 0.375

Gnomad4 OTH AF: 0.503

Alfa AF: 0.405 Hom.: 28323

Bravo AF: 0.524

Asia WGS AF: 0.677 AC: 2352 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.060
DANN	Benign	0.25

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2179367; hg19: chr6-149762537;