rs1736135

Variant names:

• chr21-15432901-T-C
• rs1736135
• ENST00000634642.1:n.343+11123A>G

Variant summary

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

The ENST00000634642.1(ENSG00000229425):​n.343+11123A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.328 in 152,118 control chromosomes in the GnomAD database, including 9,590 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 0.33 (9590 hom., cov: 32)
• Consequence: ENSG00000229425 ENST00000634642.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.916
• Publications: 56 publications found

Genes affected

ENSG00000229425 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.428 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC101927745	NR_188234.1	n.341+11123A>G		intron_variant	Intron 2 of 8
LOC101927745	NR_188235.1	n.341+11123A>G		intron_variant	Intron 2 of 6
LOC101927745	NR_188236.1	n.341+11123A>G		intron_variant	Intron 2 of 7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000229425	ENST00000634642.1	n.343+11123A>G		intron_variant	Intron 1 of 6	3
ENSG00000229425	ENST00000634644.1	n.952+34387A>G		intron_variant	Intron 8 of 11	5
ENSG00000229425	ENST00000634708.1	n.424-32352A>G		intron_variant	Intron 3 of 9	5

Frequencies

GnomAD3 genomes AF: 0.328 AC: 49856 AN: 152000 Hom.: 9587 Cov.: 32

Gnomad AFR AF: 0.127

Gnomad AMI AF: 0.584

Gnomad AMR AF: 0.388

Gnomad ASJ AF: 0.305

Gnomad EAS AF: 0.188

Gnomad SAS AF: 0.351

Gnomad FIN AF: 0.394

Gnomad MID AF: 0.456

Gnomad NFE AF: 0.432

Gnomad OTH AF: 0.358

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

GnomAD4 genome AF: 0.328 AC: 49863 AN: 152118 Hom.: 9590 Cov.: 32 AF XY: 0.324 AC XY: 24101 AN XY: 74342

African (AFR) AF: 0.127 AC: 5269 AN: 41506

American (AMR) AF: 0.388 AC: 5929 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.305 AC: 1059 AN: 3468

East Asian (EAS) AF: 0.188 AC: 975 AN: 5184

South Asian (SAS) AF: 0.351 AC: 1694 AN: 4822

European-Finnish (FIN) AF: 0.394 AC: 4164 AN: 10558

Middle Eastern (MID) AF: 0.442 AC: 130 AN: 294

European-Non Finnish (NFE) AF: 0.432 AC: 29357 AN: 67986

Other (OTH) AF: 0.357 AC: 755 AN: 2114

Alfa AF: 0.389 Hom.: 48338

Bravo AF: 0.320

Asia WGS AF: 0.311 AC: 1076 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	11
DANN	Benign	0.69
PhyloP100		0.92

Splicing

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

Other links and lift over

dbSNP: rs1736135; hg19: chr21-16805220;