chr2-136256036-C-T

Variant names:

• chr2-136256036-C-T
• rs10221893
• ENST00000837573.1:n.120+9511C>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+9511C>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 152,066 control chromosomes in the GnomAD database, including 14,503 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 (14503 hom., cov: 33)
• Consequence: ENSG00000308974 ENST00000837573.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.950
• Publications: 9 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=-0.84).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.563 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000837573.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000308974	ENST00000837573.1		n.120+9511C>T		intron	N/A
	ENSG00000308974	ENST00000837574.1		n.284+1892C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.370 AC: 56190 AN: 151948 Hom.: 14507 Cov.: 33

Gnomad AFR AF: 0.112

Gnomad AMI AF: 0.570

Gnomad AMR AF: 0.222

Gnomad ASJ AF: 0.174

Gnomad EAS AF: 0.0272

Gnomad SAS AF: 0.238

Gnomad FIN AF: 0.619

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: 56177 AN: 152066 Hom.: 14503 Cov.: 33 AF XY: 0.362 AC XY: 26890 AN XY: 74322

African (AFR) AF: 0.111 AC: 4622 AN: 41488

American (AMR) AF: 0.222 AC: 3388 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.174 AC: 602 AN: 3468

East Asian (EAS) AF: 0.0270 AC: 140 AN: 5176

South Asian (SAS) AF: 0.239 AC: 1150 AN: 4818

European-Finnish (FIN) AF: 0.619 AC: 6529 AN: 10550

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

European-Non Finnish (NFE) AF: 0.568 AC: 38624 AN: 67972

Other (OTH) AF: 0.271 AC: 571 AN: 2110

Alfa AF: 0.468 Hom.: 31211

Bravo AF: 0.327

Asia WGS AF: 0.124 AC: 434 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	1.4
DANN	Benign	0.64
PhyloP100		-0.95

Splicing

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

Other links and lift over

dbSNP: rs10221893; hg19: chr2-137013606; COSMIC: COSV50635111;