2-21810655-C-T

Variant names:

• chr2-21810655-C-T
• rs10495722
• ENST00000435237.1:n.315+11177C>T

Variant summary

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

The ENST00000435237.1(ENSG00000231204):​n.315+11177C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.386 in 151,950 control chromosomes in the GnomAD database, including 11,879 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 0.39 (11879 hom., cov: 32)
• Consequence: ENSG00000231204 ENST00000435237.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.958
• Publications: 7 publications found

Genes affected

ENSG00000231204 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.474 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
ENSG00000231204	ENST00000435237.1	n.315+11177C>T		intron_variant	Intron 4 of 5	3

Frequencies

GnomAD3 genomes AF: 0.386 AC: 58681 AN: 151832 Hom.: 11880 Cov.: 32

Gnomad AFR AF: 0.480

Gnomad AMI AF: 0.330

Gnomad AMR AF: 0.308

Gnomad ASJ AF: 0.290

Gnomad EAS AF: 0.128

Gnomad SAS AF: 0.297

Gnomad FIN AF: 0.411

Gnomad MID AF: 0.269

Gnomad NFE AF: 0.377

Gnomad OTH AF: 0.349

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

GnomAD4 genome AF: 0.386 AC: 58707 AN: 151950 Hom.: 11879 Cov.: 32 AF XY: 0.383 AC XY: 28434 AN XY: 74224

African (AFR) AF: 0.480 AC: 19881 AN: 41456

American (AMR) AF: 0.308 AC: 4695 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.290 AC: 1006 AN: 3470

East Asian (EAS) AF: 0.128 AC: 657 AN: 5146

South Asian (SAS) AF: 0.296 AC: 1427 AN: 4818

European-Finnish (FIN) AF: 0.411 AC: 4336 AN: 10554

Middle Eastern (MID) AF: 0.279 AC: 82 AN: 294

European-Non Finnish (NFE) AF: 0.377 AC: 25592 AN: 67944

Other (OTH) AF: 0.347 AC: 730 AN: 2104

Alfa AF: 0.366 Hom.: 18083

Bravo AF: 0.382

Asia WGS AF: 0.220 AC: 767 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.82
DANN	Benign	0.53
PhyloP100		-0.96

Splicing

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

Other links and lift over

dbSNP: rs10495722; hg19: chr2-22033527;