rs2419603

Variant names:

• chr10-112144109-C-T
• rs2419603
• ENST00000727646.1:n.146-1536C>T

Variant summary

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

The ENST00000727646.1(ENSG00000295048):​n.146-1536C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.12 in 152,160 control chromosomes in the GnomAD database, including 1,189 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 0.12 (1189 hom., cov: 33)
• Consequence: ENSG00000295048 ENST00000727646.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.464
• Publications: 4 publications found

Genes affected

ENSG00000295048 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.171 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
ENSG00000295048	ENST00000727646.1	n.146-1536C>T		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.120 AC: 18262 AN: 152042 Hom.: 1185 Cov.: 33

Gnomad AFR AF: 0.174

Gnomad AMI AF: 0.119

Gnomad AMR AF: 0.0822

Gnomad ASJ AF: 0.0639

Gnomad EAS AF: 0.00212

Gnomad SAS AF: 0.107

Gnomad FIN AF: 0.117

Gnomad MID AF: 0.137

Gnomad NFE AF: 0.109

Gnomad OTH AF: 0.125

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

GnomAD4 genome AF: 0.120 AC: 18288 AN: 152160 Hom.: 1189 Cov.: 33 AF XY: 0.119 AC XY: 8848 AN XY: 74382

African (AFR) AF: 0.174 AC: 7233 AN: 41478

American (AMR) AF: 0.0819 AC: 1252 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.0639 AC: 222 AN: 3472

East Asian (EAS) AF: 0.00193 AC: 10 AN: 5186

South Asian (SAS) AF: 0.107 AC: 516 AN: 4820

European-Finnish (FIN) AF: 0.117 AC: 1234 AN: 10584

Middle Eastern (MID) AF: 0.140 AC: 41 AN: 292

European-Non Finnish (NFE) AF: 0.109 AC: 7406 AN: 68008

Other (OTH) AF: 0.126 AC: 266 AN: 2114

Alfa AF: 0.114 Hom.: 1408

Bravo AF: 0.120

Asia WGS AF: 0.0730 AC: 257 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	5.2
DANN	Benign	0.42
PhyloP100		0.46

Splicing

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

Other links and lift over

dbSNP: rs2419603; hg19: chr10-113903867;