2-56121594-C-T

Variant names:

• chr2-56121594-C-T
• rs11885285
• ENST00000606639.1:n.160-26036C>T

Variant summary

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

The ENST00000606639.1(ENSG00000272180):​n.160-26036C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.196 in 152,018 control chromosomes in the GnomAD database, including 3,013 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 0.20 (3013 hom., cov: 31)
• Consequence: ENSG00000272180 ENST00000606639.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.04
• Publications: 1 publications found

Genes affected

ENSG00000272180 (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 (SAS) allele frequency at 95% confidence interval = 0.299 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105374690	XR_940109.3	n.778+3423C>T		intron_variant	Intron 5 of 8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000272180	ENST00000606639.1	n.160-26036C>T		intron_variant	Intron 2 of 6	1
ENSG00000271894	ENST00000607540.2	n.90+3423C>T		intron_variant	Intron 1 of 4	5
ENSG00000272180	ENST00000717251.1	n.211+3423C>T		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.196 AC: 29820 AN: 151900 Hom.: 3012 Cov.: 31

Gnomad AFR AF: 0.170

Gnomad AMI AF: 0.240

Gnomad AMR AF: 0.163

Gnomad ASJ AF: 0.200

Gnomad EAS AF: 0.161

Gnomad SAS AF: 0.312

Gnomad FIN AF: 0.178

Gnomad MID AF: 0.171

Gnomad NFE AF: 0.217

Gnomad OTH AF: 0.201

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

GnomAD4 genome AF: 0.196 AC: 29840 AN: 152018 Hom.: 3013 Cov.: 31 AF XY: 0.197 AC XY: 14618 AN XY: 74314

African (AFR) AF: 0.170 AC: 7037 AN: 41486

American (AMR) AF: 0.163 AC: 2492 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.200 AC: 695 AN: 3468

East Asian (EAS) AF: 0.161 AC: 830 AN: 5152

South Asian (SAS) AF: 0.312 AC: 1496 AN: 4798

European-Finnish (FIN) AF: 0.178 AC: 1880 AN: 10580

Middle Eastern (MID) AF: 0.163 AC: 48 AN: 294

European-Non Finnish (NFE) AF: 0.217 AC: 14724 AN: 67942

Other (OTH) AF: 0.199 AC: 419 AN: 2106

Alfa AF: 0.192 Hom.: 1979

Bravo AF: 0.189

Asia WGS AF: 0.239 AC: 833 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.11
DANN	Benign	0.81
PhyloP100		-3.0
Mutation Taster		=100/0	polymorphism

Splicing

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

Other links and lift over

dbSNP: rs11885285; hg19: chr2-56348729;