rs6534349

Positions:

• chr4-122481040-A-G

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

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

Gnomad4 AFR AF: 0.389

Gnomad4 AMR AF: 0.0835

Gnomad4 ASJ AF: 0.0544

Gnomad4 EAS AF: 0.00231

Gnomad4 SAS AF: 0.0616

Gnomad4 FIN AF: 0.0950

Gnomad4 NFE AF: 0.0822

Gnomad4 OTH AF: 0.139

Alfa AF: 0.134 Hom.: 310

Bravo AF: 0.170

Asia WGS AF: 0.0540 AC: 190 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6534349; hg19: chr4-123402195;