6-138130137-G-A

Variant names:

• chr6-138130137-G-A
• rs4896318

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 0.352 in 152,052 control chromosomes in the GnomAD database, including 9,947 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 0.35 (9947 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.612
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.71 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: 0.351 AC: 53372 AN: 151934 Hom.: 9913 Cov.: 32

Gnomad AFR AF: 0.308

Gnomad AMI AF: 0.254

Gnomad AMR AF: 0.390

Gnomad ASJ AF: 0.347

Gnomad EAS AF: 0.729

Gnomad SAS AF: 0.468

Gnomad FIN AF: 0.290

Gnomad MID AF: 0.345

Gnomad NFE AF: 0.343

Gnomad OTH AF: 0.346

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

GnomAD4 genome AF: 0.352 AC: 53447 AN: 152052 Hom.: 9947 Cov.: 32 AF XY: 0.353 AC XY: 26200 AN XY: 74316

African (AFR) AF: 0.309 AC: 12811 AN: 41470

American (AMR) AF: 0.391 AC: 5971 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.347 AC: 1202 AN: 3464

East Asian (EAS) AF: 0.729 AC: 3766 AN: 5166

South Asian (SAS) AF: 0.468 AC: 2254 AN: 4816

European-Finnish (FIN) AF: 0.290 AC: 3066 AN: 10564

Middle Eastern (MID) AF: 0.327 AC: 96 AN: 294

European-Non Finnish (NFE) AF: 0.343 AC: 23304 AN: 67966

Other (OTH) AF: 0.353 AC: 746 AN: 2112

Alfa AF: 0.338 Hom.: 14637

Bravo AF: 0.356

Asia WGS AF: 0.568 AC: 1973 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.68
DANN	Benign	0.50
PhyloP100		-0.61

Splicing

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

Other links and lift over

dbSNP: rs4896318; hg19: chr6-138451274;