2-136149559-C-T

Variant names:

• chr2-136149559-C-T
• rs953388
• ENST00000805101.1:n.685+22109C>T

Variant summary

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

The ENST00000805101.1(ENSG00000304642):​n.685+22109C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.118 in 152,102 control chromosomes in the GnomAD database, including 1,453 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 0.12 (1453 hom., cov: 32)
• Consequence: ENSG00000304642 ENST00000805101.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0650
• Publications: 7 publications found

Genes affected

ENSG00000304642 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.287 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000805101.1. 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
	ENSG00000304642	ENST00000805101.1		n.685+22109C>T		intron	N/A
	ENSG00000304642	ENST00000805102.1		n.142-6764C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.118 AC: 17934 AN: 151984 Hom.: 1457 Cov.: 32

Gnomad AFR AF: 0.0262

Gnomad AMI AF: 0.238

Gnomad AMR AF: 0.175

Gnomad ASJ AF: 0.251

Gnomad EAS AF: 0.300

Gnomad SAS AF: 0.208

Gnomad FIN AF: 0.163

Gnomad MID AF: 0.325

Gnomad NFE AF: 0.123

Gnomad OTH AF: 0.159

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

GnomAD4 genome AF: 0.118 AC: 17921 AN: 152102 Hom.: 1453 Cov.: 32 AF XY: 0.124 AC XY: 9186 AN XY: 74314

African (AFR) AF: 0.0262 AC: 1087 AN: 41528

American (AMR) AF: 0.175 AC: 2672 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.251 AC: 870 AN: 3470

East Asian (EAS) AF: 0.299 AC: 1539 AN: 5140

South Asian (SAS) AF: 0.209 AC: 1007 AN: 4818

European-Finnish (FIN) AF: 0.163 AC: 1720 AN: 10574

Middle Eastern (MID) AF: 0.312 AC: 91 AN: 292

European-Non Finnish (NFE) AF: 0.123 AC: 8384 AN: 67978

Other (OTH) AF: 0.158 AC: 334 AN: 2110

Alfa AF: 0.116 Hom.: 692

Bravo AF: 0.115

Asia WGS AF: 0.236 AC: 818 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	1.4
DANN	Benign	0.73
PhyloP100		0.065

Splicing

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

Other links and lift over

dbSNP: rs953388; hg19: chr2-136907129;