10-117581770-A-T

Variant names:

• chr10-117581770-A-T
• rs2531670
• ENST00000672708.1:n.73+1844A>T

Variant summary

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

The ENST00000672708.1(ENSG00000288172):​n.73+1844A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.465 in 152,042 control chromosomes in the GnomAD database, including 18,238 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 0.46 (18238 hom., cov: 32)
• Consequence: ENSG00000288172 ENST00000672708.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.845
• Publications: 1 publications found

Genes affected

ENSG00000288172 (HGNC:):

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 (AFR) allele frequency at 95% confidence interval = 0.686 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000672708.1. You can select a different transcript below to see updated ACMG assignments.

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
	ENSG00000288172	ENST00000672708.1		n.73+1844A>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.465 AC: 70597 AN: 151924 Hom.: 18204 Cov.: 32

Gnomad AFR AF: 0.693

Gnomad AMI AF: 0.333

Gnomad AMR AF: 0.422

Gnomad ASJ AF: 0.349

Gnomad EAS AF: 0.479

Gnomad SAS AF: 0.464

Gnomad FIN AF: 0.400

Gnomad MID AF: 0.310

Gnomad NFE AF: 0.355

Gnomad OTH AF: 0.409

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

GnomAD4 genome AF: 0.465 AC: 70683 AN: 152042 Hom.: 18238 Cov.: 32 AF XY: 0.465 AC XY: 34569 AN XY: 74316

African (AFR) AF: 0.693 AC: 28727 AN: 41472

American (AMR) AF: 0.423 AC: 6464 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.349 AC: 1206 AN: 3458

East Asian (EAS) AF: 0.479 AC: 2475 AN: 5164

South Asian (SAS) AF: 0.464 AC: 2227 AN: 4804

European-Finnish (FIN) AF: 0.400 AC: 4229 AN: 10568

Middle Eastern (MID) AF: 0.320 AC: 94 AN: 294

European-Non Finnish (NFE) AF: 0.355 AC: 24103 AN: 67972

Other (OTH) AF: 0.404 AC: 854 AN: 2116

Alfa AF: 0.268 Hom.: 664

Bravo AF: 0.474

Asia WGS AF: 0.489 AC: 1699 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	7.6
DANN	Benign	0.46
PhyloP100		0.84

Splicing

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

Other links and lift over

dbSNP: rs2531670; hg19: chr10-119341281;