ENST00000673857.1:n.63-10400T>G

Variant names:

• chr6-31452723-T-G
• rs3131622
• ENST00000673857.1:n.63-10400T>G

Variant summary

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

The ENST00000673857.1(ENSG00000288587):​n.63-10400T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.404 in 151,654 control chromosomes in the GnomAD database, including 13,056 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 0.40 (13056 hom., cov: 32)
• Consequence: ENSG00000288587 ENST00000673857.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0970
• Publications: 27 publications found

Genes affected

ENSG00000288587 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.418 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
ENSG00000288587	ENST00000673857.1	n.63-10400T>G		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.404 AC: 61167 AN: 151534 Hom.: 13042 Cov.: 32

Gnomad AFR AF: 0.370

Gnomad AMI AF: 0.607

Gnomad AMR AF: 0.420

Gnomad ASJ AF: 0.479

Gnomad EAS AF: 0.201

Gnomad SAS AF: 0.351

Gnomad FIN AF: 0.481

Gnomad MID AF: 0.373

Gnomad NFE AF: 0.422

Gnomad OTH AF: 0.385

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

GnomAD4 genome AF: 0.404 AC: 61223 AN: 151654 Hom.: 13056 Cov.: 32 AF XY: 0.401 AC XY: 29756 AN XY: 74114

African (AFR) AF: 0.370 AC: 15259 AN: 41242

American (AMR) AF: 0.420 AC: 6381 AN: 15178

Ashkenazi Jewish (ASJ) AF: 0.479 AC: 1658 AN: 3464

East Asian (EAS) AF: 0.201 AC: 1037 AN: 5168

South Asian (SAS) AF: 0.353 AC: 1695 AN: 4808

European-Finnish (FIN) AF: 0.481 AC: 5072 AN: 10552

Middle Eastern (MID) AF: 0.366 AC: 107 AN: 292

European-Non Finnish (NFE) AF: 0.422 AC: 28663 AN: 67942

Other (OTH) AF: 0.381 AC: 799 AN: 2098

Alfa AF: 0.414 Hom.: 27771

Bravo AF: 0.397

Asia WGS AF: 0.279 AC: 972 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	5.5
DANN	Benign	0.46
PhyloP100		0.097

Splicing

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

Other links and lift over

dbSNP: rs3131622; hg19: chr6-31420500;