rs2256543

chr6-29970056-T-C

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 0.596 in 151,194 control chromosomes in the GnomAD database, including 27,132 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 0.60 (27132 hom., cov: 29)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.24

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.724 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.596 AC: 90000 AN: 151086 Hom.: 27084 Cov.: 29

Gnomad AFR AF: 0.611

Gnomad AMI AF: 0.517

Gnomad AMR AF: 0.637

Gnomad ASJ AF: 0.642

Gnomad EAS AF: 0.743

Gnomad SAS AF: 0.637

Gnomad FIN AF: 0.562

Gnomad MID AF: 0.592

Gnomad NFE AF: 0.567

Gnomad OTH AF: 0.602

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

GnomAD4 genome AF: 0.596 AC: 90087 AN: 151194 Hom.: 27132 Cov.: 29 AF XY: 0.598 AC XY: 44157 AN XY: 73898

Gnomad4 AFR AF: 0.611

Gnomad4 AMR AF: 0.637

Gnomad4 ASJ AF: 0.642

Gnomad4 EAS AF: 0.743

Gnomad4 SAS AF: 0.640

Gnomad4 FIN AF: 0.562

Gnomad4 NFE AF: 0.567

Gnomad4 OTH AF: 0.598

Alfa AF: 0.585 Hom.: 22345

Bravo AF: 0.603

Asia WGS AF: 0.607 AC: 2090 AN: 3448

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	3.0
Dann	Benign	0.35

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2256543; hg19: chr6-29937833;