6-149441401-A-G

Variant names:

• chr6-149441401-A-G
• rs2179367

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 20 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.691 AC: 28623 AN: 41400

American (AMR) AF: 0.548 AC: 8356 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.426 AC: 1476 AN: 3468

East Asian (EAS) AF: 0.750 AC: 3857 AN: 5140

South Asian (SAS) AF: 0.518 AC: 2478 AN: 4782

European-Finnish (FIN) AF: 0.391 AC: 4129 AN: 10558

Middle Eastern (MID) AF: 0.421 AC: 123 AN: 292

European-Non Finnish (NFE) AF: 0.375 AC: 25433 AN: 67892

Other (OTH) AF: 0.503 AC: 1058 AN: 2104

Alfa AF: 0.423 Hom.: 65971

Bravo AF: 0.524

Asia WGS AF: 0.677 AC: 2352 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.060
DANN	Benign	0.25
PhyloP100		-1.8

Splicing

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

Other links and lift over

dbSNP: rs2179367; hg19: chr6-149762537;