chr6-129760916-G-A

Variant names:

• chr6-129760916-G-A
• rs4897336

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 0.135 in 152,132 control chromosomes in the GnomAD database, including 2,031 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 0.13 (2031 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.25
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.49 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: 0.135 AC: 20480 AN: 152014 Hom.: 2026 Cov.: 32

Gnomad AFR AF: 0.154

Gnomad AMI AF: 0.0461

Gnomad AMR AF: 0.206

Gnomad ASJ AF: 0.141

Gnomad EAS AF: 0.506

Gnomad SAS AF: 0.171

Gnomad FIN AF: 0.0923

Gnomad MID AF: 0.155

Gnomad NFE AF: 0.0837

Gnomad OTH AF: 0.136

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

GnomAD4 genome AF: 0.135 AC: 20503 AN: 152132 Hom.: 2031 Cov.: 32 AF XY: 0.138 AC XY: 10284 AN XY: 74360

African (AFR) AF: 0.154 AC: 6388 AN: 41502

American (AMR) AF: 0.207 AC: 3162 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.141 AC: 490 AN: 3472

East Asian (EAS) AF: 0.506 AC: 2607 AN: 5148

South Asian (SAS) AF: 0.169 AC: 816 AN: 4828

European-Finnish (FIN) AF: 0.0923 AC: 978 AN: 10596

Middle Eastern (MID) AF: 0.156 AC: 46 AN: 294

European-Non Finnish (NFE) AF: 0.0837 AC: 5688 AN: 67980

Other (OTH) AF: 0.136 AC: 286 AN: 2110

Alfa AF: 0.104 Hom.: 3146

Bravo AF: 0.148

Asia WGS AF: 0.334 AC: 1159 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	5.9
DANN	Benign	0.42
PhyloP100		1.3

Splicing

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

Other links and lift over

dbSNP: rs4897336; hg19: chr6-130082061;