6-149419535-A-G

Variant names:

• chr6-149419535-A-G
• rs513923

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 0.175 in 152,182 control chromosomes in the GnomAD database, including 2,966 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 0.17 (2966 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.688
• Publications: 6 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.496 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: 0.175 AC: 26546 AN: 152064 Hom.: 2962 Cov.: 32

Gnomad AFR AF: 0.246

Gnomad AMI AF: 0.00440

Gnomad AMR AF: 0.225

Gnomad ASJ AF: 0.127

Gnomad EAS AF: 0.513

Gnomad SAS AF: 0.212

Gnomad FIN AF: 0.122

Gnomad MID AF: 0.120

Gnomad NFE AF: 0.105

Gnomad OTH AF: 0.163

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

GnomAD4 genome AF: 0.175 AC: 26576 AN: 152182 Hom.: 2966 Cov.: 32 AF XY: 0.178 AC XY: 13237 AN XY: 74394

African (AFR) AF: 0.246 AC: 10187 AN: 41488

American (AMR) AF: 0.226 AC: 3452 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.127 AC: 440 AN: 3464

East Asian (EAS) AF: 0.513 AC: 2656 AN: 5182

South Asian (SAS) AF: 0.212 AC: 1021 AN: 4820

European-Finnish (FIN) AF: 0.122 AC: 1290 AN: 10606

Middle Eastern (MID) AF: 0.126 AC: 37 AN: 294

European-Non Finnish (NFE) AF: 0.105 AC: 7148 AN: 68018

Other (OTH) AF: 0.162 AC: 341 AN: 2110

Alfa AF: 0.141 Hom.: 3056

Bravo AF: 0.190

Asia WGS AF: 0.339 AC: 1175 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	3.2
DANN	Benign	0.62
PhyloP100		-0.69

Splicing

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

Other links and lift over

dbSNP: rs513923; hg19: chr6-149740671;