ENST00000656217.1:n.133-49322A>G

Variant names:

• chr10-111838426-T-C
• rs4344422
• ENST00000656217.1:n.133-49322A>G

Variant summary

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

The ENST00000656217.1(ENSG00000287231):​n.133-49322A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.247 in 152,248 control chromosomes in the GnomAD database, including 5,609 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 0.25 (5609 hom., cov: 33)
• Consequence: ENSG00000287231 ENST00000656217.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.308
• 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=-0.97).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.342 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
ENSG00000287231	ENST00000656217.1	n.133-49322A>G		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.247 AC: 37551 AN: 152130 Hom.: 5603 Cov.: 33

Gnomad AFR AF: 0.104

Gnomad AMI AF: 0.502

Gnomad AMR AF: 0.221

Gnomad ASJ AF: 0.261

Gnomad EAS AF: 0.121

Gnomad SAS AF: 0.149

Gnomad FIN AF: 0.294

Gnomad MID AF: 0.190

Gnomad NFE AF: 0.345

Gnomad OTH AF: 0.246

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

GnomAD4 genome AF: 0.247 AC: 37559 AN: 152248 Hom.: 5609 Cov.: 33 AF XY: 0.242 AC XY: 17995 AN XY: 74428

African (AFR) AF: 0.104 AC: 4312 AN: 41566

American (AMR) AF: 0.221 AC: 3372 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.261 AC: 904 AN: 3470

East Asian (EAS) AF: 0.121 AC: 628 AN: 5188

South Asian (SAS) AF: 0.150 AC: 724 AN: 4830

European-Finnish (FIN) AF: 0.294 AC: 3110 AN: 10576

Middle Eastern (MID) AF: 0.194 AC: 57 AN: 294

European-Non Finnish (NFE) AF: 0.345 AC: 23483 AN: 68008

Other (OTH) AF: 0.242 AC: 511 AN: 2114

Alfa AF: 0.289 Hom.: 1698

Bravo AF: 0.236

Asia WGS AF: 0.137 AC: 478 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	2.2
DANN	Benign	0.47
PhyloP100		0.31

Splicing

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

Other links and lift over

dbSNP: rs4344422; hg19: chr10-113598184;