10-111846540-T-A

Variant names:

• chr10-111846540-T-A
• rs2419598
• ENST00000656217.1:n.133-57436A>T

Variant summary

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

The ENST00000656217.1(ENSG00000287231):​n.133-57436A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.491 in 152,020 control chromosomes in the GnomAD database, including 20,406 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 0.49 (20406 hom., cov: 32)
• Consequence: ENSG00000287231 ENST00000656217.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.566
• Publications: 2 publications found

Genes affected

ENSG00000287231 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.728 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000656217.1. 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
	ENSG00000287231	ENST00000656217.1		n.133-57436A>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.490 AC: 74482 AN: 151902 Hom.: 20352 Cov.: 32

Gnomad AFR AF: 0.734

Gnomad AMI AF: 0.526

Gnomad AMR AF: 0.416

Gnomad ASJ AF: 0.370

Gnomad EAS AF: 0.160

Gnomad SAS AF: 0.246

Gnomad FIN AF: 0.375

Gnomad MID AF: 0.320

Gnomad NFE AF: 0.427

Gnomad OTH AF: 0.447

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

GnomAD4 genome AF: 0.491 AC: 74597 AN: 152020 Hom.: 20406 Cov.: 32 AF XY: 0.481 AC XY: 35729 AN XY: 74320

African (AFR) AF: 0.735 AC: 30445 AN: 41448

American (AMR) AF: 0.416 AC: 6357 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.370 AC: 1284 AN: 3468

East Asian (EAS) AF: 0.161 AC: 829 AN: 5164

South Asian (SAS) AF: 0.247 AC: 1189 AN: 4820

European-Finnish (FIN) AF: 0.375 AC: 3964 AN: 10562

Middle Eastern (MID) AF: 0.316 AC: 93 AN: 294

European-Non Finnish (NFE) AF: 0.427 AC: 29025 AN: 67974

Other (OTH) AF: 0.442 AC: 932 AN: 2110

Alfa AF: 0.464 Hom.: 2199

Bravo AF: 0.503

Asia WGS AF: 0.258 AC: 898 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	1.1
DANN	Benign	0.59
PhyloP100		-0.57

Splicing

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

Other links and lift over

dbSNP: rs2419598; hg19: chr10-113606298;