rs6534349

Variant names:

• chr4-122481040-A-G
• rs6534349

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 0.163 in 152,148 control chromosomes in the GnomAD database, including 3,601 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 0.16 (3601 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.270
• Publications: 7 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.384 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.163 AC: 24837 AN: 152030 Hom.: 3588 Cov.: 32

Gnomad AFR AF: 0.389

Gnomad AMI AF: 0.0417

Gnomad AMR AF: 0.0837

Gnomad ASJ AF: 0.0544

Gnomad EAS AF: 0.00231

Gnomad SAS AF: 0.0626

Gnomad FIN AF: 0.0950

Gnomad MID AF: 0.108

Gnomad NFE AF: 0.0823

Gnomad OTH AF: 0.142

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

GnomAD4 genome AF: 0.163 AC: 24875 AN: 152148 Hom.: 3601 Cov.: 32 AF XY: 0.161 AC XY: 12011 AN XY: 74394

African (AFR) AF: 0.389 AC: 16142 AN: 41464

American (AMR) AF: 0.0835 AC: 1275 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.0544 AC: 189 AN: 3472

East Asian (EAS) AF: 0.00231 AC: 12 AN: 5194

South Asian (SAS) AF: 0.0616 AC: 297 AN: 4824

European-Finnish (FIN) AF: 0.0950 AC: 1007 AN: 10600

Middle Eastern (MID) AF: 0.0952 AC: 28 AN: 294

European-Non Finnish (NFE) AF: 0.0822 AC: 5593 AN: 68004

Other (OTH) AF: 0.139 AC: 294 AN: 2112

Alfa AF: 0.143 Hom.: 367

Bravo AF: 0.170

Asia WGS AF: 0.0540 AC: 190 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	3.7
DANN	Benign	0.59
PhyloP100		0.27

Splicing

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

Other links and lift over

dbSNP: rs6534349; hg19: chr4-123402195;