2-56136242-T-C

Variant names:

• chr2-56136242-T-C
• rs6751715
• ENST00000606639.1:n.160-11388T>C

Variant summary

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

The ENST00000606639.1(ENSG00000272180):​n.160-11388T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.389 in 152,006 control chromosomes in the GnomAD database, including 12,145 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 0.39 (12145 hom., cov: 31)
• Consequence: ENSG00000272180 ENST00000606639.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.149
• Publications: 9 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=-1.0).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.496 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000606639.1. 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
	ENSG00000272180	ENST00000606639.1	TSL:1	n.160-11388T>C		intron	N/A
	ENSG00000271894	ENST00000607540.2	TSL:5	n.91-11388T>C		intron	N/A
	ENSG00000272180	ENST00000717251.1		n.212-11388T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.389 AC: 59097 AN: 151888 Hom.: 12136 Cov.: 31

Gnomad AFR AF: 0.283

Gnomad AMI AF: 0.556

Gnomad AMR AF: 0.505

Gnomad ASJ AF: 0.352

Gnomad EAS AF: 0.212

Gnomad SAS AF: 0.457

Gnomad FIN AF: 0.387

Gnomad MID AF: 0.335

Gnomad NFE AF: 0.437

Gnomad OTH AF: 0.386

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

GnomAD4 genome AF: 0.389 AC: 59145 AN: 152006 Hom.: 12145 Cov.: 31 AF XY: 0.391 AC XY: 29022 AN XY: 74294

African (AFR) AF: 0.283 AC: 11727 AN: 41460

American (AMR) AF: 0.506 AC: 7715 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.352 AC: 1221 AN: 3468

East Asian (EAS) AF: 0.212 AC: 1095 AN: 5170

South Asian (SAS) AF: 0.457 AC: 2201 AN: 4818

European-Finnish (FIN) AF: 0.387 AC: 4089 AN: 10568

Middle Eastern (MID) AF: 0.330 AC: 97 AN: 294

European-Non Finnish (NFE) AF: 0.437 AC: 29682 AN: 67950

Other (OTH) AF: 0.384 AC: 811 AN: 2110

Alfa AF: 0.419 Hom.: 44577

Bravo AF: 0.395

Asia WGS AF: 0.360 AC: 1251 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.8
DANN	Benign	0.56
PhyloP100		-0.15

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs6751715;

hg19: chr2-56363377;