2-136256331-C-T

Variant names:

• chr2-136256331-C-T
• rs4072435
• ENST00000837573.1:n.120+9806C>T

Variant summary

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

The ENST00000837573.1(ENSG00000308974):​n.120+9806C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.369 in 152,192 control chromosomes in the GnomAD database, including 14,502 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 0.37 (14502 hom., cov: 33)
• Consequence: ENSG00000308974 ENST00000837573.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.10
• Publications: 4 publications found

Genes affected

ENSG00000308974 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.67).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.563 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
ENSG00000308974	ENST00000837573.1	n.120+9806C>T		intron_variant	Intron 1 of 1
ENSG00000308974	ENST00000837574.1	n.284+2187C>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.369 AC: 56187 AN: 152074 Hom.: 14506 Cov.: 33

Gnomad AFR AF: 0.111

Gnomad AMI AF: 0.570

Gnomad AMR AF: 0.222

Gnomad ASJ AF: 0.173

Gnomad EAS AF: 0.0275

Gnomad SAS AF: 0.238

Gnomad FIN AF: 0.618

Gnomad MID AF: 0.104

Gnomad NFE AF: 0.568

Gnomad OTH AF: 0.274

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

GnomAD4 genome AF: 0.369 AC: 56174 AN: 152192 Hom.: 14502 Cov.: 33 AF XY: 0.361 AC XY: 26899 AN XY: 74414

African (AFR) AF: 0.111 AC: 4622 AN: 41562

American (AMR) AF: 0.221 AC: 3388 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.173 AC: 602 AN: 3472

East Asian (EAS) AF: 0.0274 AC: 142 AN: 5180

South Asian (SAS) AF: 0.239 AC: 1152 AN: 4830

European-Finnish (FIN) AF: 0.618 AC: 6537 AN: 10574

Middle Eastern (MID) AF: 0.105 AC: 31 AN: 294

European-Non Finnish (NFE) AF: 0.568 AC: 38611 AN: 67962

Other (OTH) AF: 0.270 AC: 571 AN: 2114

Alfa AF: 0.457 Hom.: 5097

Bravo AF: 0.327

Asia WGS AF: 0.124 AC: 433 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.67
CADD	Benign	12
DANN	Benign	0.87
PhyloP100		1.1

Splicing

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

Other links and lift over

dbSNP: rs4072435; hg19: chr2-137013901;