ENST00000606639.1:n.160-11388T>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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105374690	XR_940109.3	n.779-11388T>C		intron_variant	Intron 5 of 8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000272180	ENST00000606639.1	n.160-11388T>C		intron_variant	Intron 2 of 6	1
ENSG00000271894	ENST00000607540.2	n.91-11388T>C		intron_variant	Intron 1 of 4	5
ENSG00000272180	ENST00000717251.1	n.212-11388T>C		intron_variant	Intron 1 of 3

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 v4.3

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

Other links and lift over

dbSNP: rs6751715; hg19: chr2-56363377;