6-31222526-T-C

Position:

• chr6-31222526-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 0.288 in 152,182 control chromosomes in the GnomAD database, including 6,429 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 0.29 (6429 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.281

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.382 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: 0.288 AC: 43825 AN: 152062 Hom.: 6425 Cov.: 32

Gnomad AFR AF: 0.324

Gnomad AMI AF: 0.368

Gnomad AMR AF: 0.244

Gnomad ASJ AF: 0.310

Gnomad EAS AF: 0.396

Gnomad SAS AF: 0.318

Gnomad FIN AF: 0.182

Gnomad MID AF: 0.294

Gnomad NFE AF: 0.280

Gnomad OTH AF: 0.288

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

GnomAD4 genome AF: 0.288 AC: 43854 AN: 152182 Hom.: 6429 Cov.: 32 AF XY: 0.283 AC XY: 21040 AN XY: 74408

Gnomad4 AFR AF: 0.324

Gnomad4 AMR AF: 0.244

Gnomad4 ASJ AF: 0.310

Gnomad4 EAS AF: 0.396

Gnomad4 SAS AF: 0.317

Gnomad4 FIN AF: 0.182

Gnomad4 NFE AF: 0.280

Gnomad4 OTH AF: 0.288

Alfa AF: 0.287 Hom.: 8613

Bravo AF: 0.293

Asia WGS AF: 0.296 AC: 1032 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	4.9
DANN	Benign	0.80

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3130517; hg19: chr6-31190303;