6-31100249-C-A

Variant names:

• chr6-31100249-C-A
• rs74992754

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 0.16 in 152,118 control chromosomes in the GnomAD database, including 2,212 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 (2212 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0550

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.359 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: 0.160 AC: 24272 AN: 152000 Hom.: 2215 Cov.: 32

Gnomad AFR AF: 0.102

Gnomad AMI AF: 0.156

Gnomad AMR AF: 0.164

Gnomad ASJ AF: 0.141

Gnomad EAS AF: 0.373

Gnomad SAS AF: 0.275

Gnomad FIN AF: 0.139

Gnomad MID AF: 0.172

Gnomad NFE AF: 0.174

Gnomad OTH AF: 0.158

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

GnomAD4 genome AF: 0.160 AC: 24282 AN: 152118 Hom.: 2212 Cov.: 32 AF XY: 0.161 AC XY: 11955 AN XY: 74356

Gnomad4 AFR AF: 0.102

Gnomad4 AMR AF: 0.163

Gnomad4 ASJ AF: 0.141

Gnomad4 EAS AF: 0.373

Gnomad4 SAS AF: 0.275

Gnomad4 FIN AF: 0.139

Gnomad4 NFE AF: 0.174

Gnomad4 OTH AF: 0.158

Alfa AF: 0.160 Hom.: 1462

Bravo AF: 0.155

Asia WGS AF: 0.280 AC: 973 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	2.1
DANN	Benign	0.51

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs74992754; hg19: chr6-31068026;