rs2256919

chr6-29972973-C-Achr6-29972973-C-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 0.547 in 152,050 control chromosomes in the GnomAD database, including 23,186 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 0.55 (23186 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.04

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.589 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: 0.547 AC: 83098 AN: 151932 Hom.: 23183 Cov.: 32

Gnomad AFR AF: 0.459

Gnomad AMI AF: 0.719

Gnomad AMR AF: 0.510

Gnomad ASJ AF: 0.445

Gnomad EAS AF: 0.563

Gnomad SAS AF: 0.476

Gnomad FIN AF: 0.690

Gnomad MID AF: 0.532

Gnomad NFE AF: 0.594

Gnomad OTH AF: 0.512

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

GnomAD4 genome AF: 0.547 AC: 83114 AN: 152050 Hom.: 23186 Cov.: 32 AF XY: 0.547 AC XY: 40652 AN XY: 74332

Gnomad4 AFR AF: 0.459

Gnomad4 AMR AF: 0.510

Gnomad4 ASJ AF: 0.445

Gnomad4 EAS AF: 0.563

Gnomad4 SAS AF: 0.472

Gnomad4 FIN AF: 0.690

Gnomad4 NFE AF: 0.594

Gnomad4 OTH AF: 0.517

Alfa AF: 0.575 Hom.: 24623

Bravo AF: 0.533

Asia WGS AF: 0.556 AC: 1935 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
Cadd	Benign	1.5
Dann	Benign	0.57

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2256919; hg19: chr6-29940750;