chr6-29970056-T-C

Variant names:

• chr6-29970056-T-C
• rs2256543

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;