rs2516464

Positions:

• chr6-31448379-A-G
• chr6-31448379-A-T

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 0.511 in 151,852 control chromosomes in the GnomAD database, including 20,615 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 0.51 (20615 hom., cov: 33)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.316

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.58).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.56 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.31448379A>G		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000288587	ENST00000673857.1	n.63-14744A>G		intron_variant

Frequencies

GnomAD3 genomes AF: 0.511 AC: 77544 AN: 151734 Hom.: 20581 Cov.: 33

Gnomad AFR AF: 0.565

Gnomad AMI AF: 0.640

Gnomad AMR AF: 0.546

Gnomad ASJ AF: 0.562

Gnomad EAS AF: 0.211

Gnomad SAS AF: 0.437

Gnomad FIN AF: 0.493

Gnomad MID AF: 0.478

Gnomad NFE AF: 0.497

Gnomad OTH AF: 0.523

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

GnomAD4 genome AF: 0.511 AC: 77617 AN: 151852 Hom.: 20615 Cov.: 33 AF XY: 0.506 AC XY: 37551 AN XY: 74222

Gnomad4 AFR AF: 0.566

Gnomad4 AMR AF: 0.546

Gnomad4 ASJ AF: 0.562

Gnomad4 EAS AF: 0.211

Gnomad4 SAS AF: 0.439

Gnomad4 FIN AF: 0.493

Gnomad4 NFE AF: 0.497

Gnomad4 OTH AF: 0.517

Alfa AF: 0.496 Hom.: 19698

Bravo AF: 0.518

Asia WGS AF: 0.343 AC: 1191 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.58
CADD	Benign	13
DANN	Benign	0.96

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2516464; hg19: chr6-31416156;