6-31250550-T-C

Variant names:

• chr6-31250550-T-C
• rs3130425

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.529 in 152,070 control chromosomes in the GnomAD database, including 21,395 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 0.53 (21395 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.229
• Publications: 14 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.554 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.529 AC: 80384 AN: 151952 Hom.: 21386 Cov.: 32

Gnomad AFR AF: 0.511

Gnomad AMI AF: 0.580

Gnomad AMR AF: 0.522

Gnomad ASJ AF: 0.604

Gnomad EAS AF: 0.550

Gnomad SAS AF: 0.367

Gnomad FIN AF: 0.465

Gnomad MID AF: 0.427

Gnomad NFE AF: 0.559

Gnomad OTH AF: 0.497

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

GnomAD4 genome AF: 0.529 AC: 80430 AN: 152070 Hom.: 21395 Cov.: 32 AF XY: 0.523 AC XY: 38878 AN XY: 74334

African (AFR) AF: 0.511 AC: 21160 AN: 41444

American (AMR) AF: 0.521 AC: 7972 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.604 AC: 2097 AN: 3472

East Asian (EAS) AF: 0.550 AC: 2841 AN: 5162

South Asian (SAS) AF: 0.365 AC: 1763 AN: 4832

European-Finnish (FIN) AF: 0.465 AC: 4915 AN: 10572

Middle Eastern (MID) AF: 0.415 AC: 122 AN: 294

European-Non Finnish (NFE) AF: 0.559 AC: 37979 AN: 67976

Other (OTH) AF: 0.497 AC: 1052 AN: 2116

Alfa AF: 0.544 Hom.: 28771

Bravo AF: 0.533

Asia WGS AF: 0.441 AC: 1541 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	8.2
DANN	Benign	0.49
PhyloP100		0.23

Splicing

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

Other links and lift over

dbSNP: rs3130425; hg19: chr6-31218327;