ENST00000657887.1:n.81+75016T>C

Variant names:

• chr6-120537607-T-C
• rs3936080
• ENST00000657887.1:n.81+75016T>C

Variant summary

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

The ENST00000657887.1(ENSG00000286540):​n.81+75016T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.39 in 151,894 control chromosomes in the GnomAD database, including 12,639 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 (12639 hom., cov: 31)
• Consequence: ENSG00000286540 ENST00000657887.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.102
• Publications: 2 publications found

Genes affected

ENSG00000286540 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.471 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000286540	ENST00000657887.1	n.81+75016T>C		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.391 AC: 59272 AN: 151774 Hom.: 12640 Cov.: 31

Gnomad AFR AF: 0.212

Gnomad AMI AF: 0.623

Gnomad AMR AF: 0.459

Gnomad ASJ AF: 0.425

Gnomad EAS AF: 0.369

Gnomad SAS AF: 0.439

Gnomad FIN AF: 0.392

Gnomad MID AF: 0.468

Gnomad NFE AF: 0.476

Gnomad OTH AF: 0.415

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

GnomAD4 genome AF: 0.390 AC: 59289 AN: 151894 Hom.: 12639 Cov.: 31 AF XY: 0.389 AC XY: 28849 AN XY: 74220

African (AFR) AF: 0.212 AC: 8791 AN: 41446

American (AMR) AF: 0.459 AC: 6997 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.425 AC: 1475 AN: 3470

East Asian (EAS) AF: 0.368 AC: 1897 AN: 5148

South Asian (SAS) AF: 0.439 AC: 2117 AN: 4820

European-Finnish (FIN) AF: 0.392 AC: 4129 AN: 10528

Middle Eastern (MID) AF: 0.459 AC: 135 AN: 294

European-Non Finnish (NFE) AF: 0.476 AC: 32299 AN: 67916

Other (OTH) AF: 0.417 AC: 882 AN: 2116

Alfa AF: 0.431 Hom.: 6064

Bravo AF: 0.386

Asia WGS AF: 0.372 AC: 1291 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.7
DANN	Benign	0.61
PhyloP100		-0.10

Splicing

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

Other links and lift over

dbSNP: rs3936080; hg19: chr6-120858753;