chr6-31513328-G-A

Variant names:

• chr6-31513328-G-A
• rs2516400

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 0.316 in 151,946 control chromosomes in the GnomAD database, including 7,843 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 0.32 (7843 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.609
• Publications: 36 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.366 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: 0.316 AC: 48039 AN: 151828 Hom.: 7835 Cov.: 32

Gnomad AFR AF: 0.371

Gnomad AMI AF: 0.260

Gnomad AMR AF: 0.214

Gnomad ASJ AF: 0.376

Gnomad EAS AF: 0.252

Gnomad SAS AF: 0.313

Gnomad FIN AF: 0.284

Gnomad MID AF: 0.392

Gnomad NFE AF: 0.314

Gnomad OTH AF: 0.303

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

GnomAD4 genome AF: 0.316 AC: 48081 AN: 151946 Hom.: 7843 Cov.: 32 AF XY: 0.312 AC XY: 23181 AN XY: 74272

African (AFR) AF: 0.371 AC: 15373 AN: 41416

American (AMR) AF: 0.214 AC: 3273 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.376 AC: 1303 AN: 3462

East Asian (EAS) AF: 0.252 AC: 1302 AN: 5158

South Asian (SAS) AF: 0.313 AC: 1508 AN: 4814

European-Finnish (FIN) AF: 0.284 AC: 2998 AN: 10550

Middle Eastern (MID) AF: 0.405 AC: 119 AN: 294

European-Non Finnish (NFE) AF: 0.314 AC: 21335 AN: 67956

Other (OTH) AF: 0.300 AC: 633 AN: 2110

Alfa AF: 0.326 Hom.: 19293

Bravo AF: 0.315

Asia WGS AF: 0.305 AC: 1063 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.63
DANN	Benign	0.67
PhyloP100		-0.61

Splicing

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

Other links and lift over

dbSNP: rs2516400; hg19: chr6-31481105;