rs2419598

Positions:

• chr10-111846540-T-A

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

ENSG00000287231 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000287231	ENST00000656217.1	n.133-57436A>T		intron_variant

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

Gnomad4 AFR AF: 0.735

Gnomad4 AMR AF: 0.416

Gnomad4 ASJ AF: 0.370

Gnomad4 EAS AF: 0.161

Gnomad4 SAS AF: 0.247

Gnomad4 FIN AF: 0.375

Gnomad4 NFE AF: 0.427

Gnomad4 OTH AF: 0.442

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 v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2419598; hg19: chr10-113606298;