rs10422744

Variant names:

• chr19-35356251-C-T
• rs10422744
• ENST00000716259.1:n.771-8629G>A

Variant summary

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

The ENST00000716259.1(ENSG00000288731):​n.771-8629G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.42 in 151,738 control chromosomes in the GnomAD database, including 13,548 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 0.42 (13548 hom., cov: 30)
• Consequence: ENSG00000288731 ENST00000716259.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.33
• Publications: 6 publications found

Genes affected

ENSG00000288731 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.495 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000716259.1. 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
	ENSG00000288731	ENST00000716259.1		n.771-8629G>A		intron	N/A
	ENSG00000288731	ENST00000786314.1		n.648-8629G>A		intron	N/A
	ENSG00000288731	ENST00000786315.1		n.160-8629G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.420 AC: 63681 AN: 151620 Hom.: 13542 Cov.: 30

Gnomad AFR AF: 0.440

Gnomad AMI AF: 0.387

Gnomad AMR AF: 0.466

Gnomad ASJ AF: 0.403

Gnomad EAS AF: 0.512

Gnomad SAS AF: 0.428

Gnomad FIN AF: 0.414

Gnomad MID AF: 0.513

Gnomad NFE AF: 0.392

Gnomad OTH AF: 0.428

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

GnomAD4 genome AF: 0.420 AC: 63720 AN: 151738 Hom.: 13548 Cov.: 30 AF XY: 0.422 AC XY: 31282 AN XY: 74152

African (AFR) AF: 0.439 AC: 18149 AN: 41300

American (AMR) AF: 0.466 AC: 7099 AN: 15238

Ashkenazi Jewish (ASJ) AF: 0.403 AC: 1397 AN: 3468

East Asian (EAS) AF: 0.511 AC: 2645 AN: 5172

South Asian (SAS) AF: 0.429 AC: 2063 AN: 4810

European-Finnish (FIN) AF: 0.414 AC: 4352 AN: 10524

Middle Eastern (MID) AF: 0.510 AC: 150 AN: 294

European-Non Finnish (NFE) AF: 0.392 AC: 26614 AN: 67920

Other (OTH) AF: 0.428 AC: 898 AN: 2100

Alfa AF: 0.404 Hom.: 13639

Bravo AF: 0.422

Asia WGS AF: 0.472 AC: 1638 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.31
DANN	Benign	0.52
PhyloP100		-1.3

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs10422744;

hg19: chr19-35847153;