ENST00000423987.2:n.74-1741T>C

Variant names:

• chr10-42339981-A-G
• rs12246221
• ENST00000423987.2:n.74-1741T>C

Variant summary

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

The ENST00000423987.2(ENSG00000215146):​n.74-1741T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.21 in 152,050 control chromosomes in the GnomAD database, including 3,909 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 0.21 (3909 hom., cov: 33)
• Consequence: ENSG00000215146 ENST00000423987.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.17
• Publications: 2 publications found

Genes affected

ENSG00000215146 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.323 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC441666	NR_024380.1	n.286+520T>C		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000215146	ENST00000423987.2	n.74-1741T>C		intron_variant	Intron 1 of 1	6
ENSG00000291065	ENST00000609034.2	n.212-1741T>C		intron_variant	Intron 1 of 1	3
ENSG00000291065	ENST00000609841.1	n.215+520T>C		intron_variant	Intron 2 of 2	4

Frequencies

GnomAD3 genomes AF: 0.210 AC: 31925 AN: 151932 Hom.: 3895 Cov.: 33

Gnomad AFR AF: 0.327

Gnomad AMI AF: 0.337

Gnomad AMR AF: 0.166

Gnomad ASJ AF: 0.193

Gnomad EAS AF: 0.325

Gnomad SAS AF: 0.211

Gnomad FIN AF: 0.0935

Gnomad MID AF: 0.263

Gnomad NFE AF: 0.156

Gnomad OTH AF: 0.236

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

GnomAD4 genome AF: 0.210 AC: 31969 AN: 152050 Hom.: 3909 Cov.: 33 AF XY: 0.206 AC XY: 15339 AN XY: 74338

African (AFR) AF: 0.327 AC: 13564 AN: 41466

American (AMR) AF: 0.166 AC: 2532 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.193 AC: 669 AN: 3468

East Asian (EAS) AF: 0.325 AC: 1681 AN: 5168

South Asian (SAS) AF: 0.209 AC: 1009 AN: 4822

European-Finnish (FIN) AF: 0.0935 AC: 987 AN: 10552

Middle Eastern (MID) AF: 0.252 AC: 74 AN: 294

European-Non Finnish (NFE) AF: 0.157 AC: 10639 AN: 67980

Other (OTH) AF: 0.240 AC: 507 AN: 2116

Alfa AF: 0.101 Hom.: 172

Bravo AF: 0.221

Asia WGS AF: 0.336 AC: 1162 AN: 3464

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	2.7
DANN	Benign	0.41
PhyloP100		-2.2

Splicing

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

Other links and lift over

dbSNP: rs12246221; hg19: chr10-42835429;