ENST00000764486.1:n.67+2142C>T

Variant names:

• chr6-79764855-C-T
• rs932492
• ENST00000764486.1:n.67+2142C>T

Variant summary

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

The ENST00000764486.1(ENSG00000299545):​n.67+2142C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.574 in 152,016 control chromosomes in the GnomAD database, including 25,572 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 0.57 (25572 hom., cov: 32)
• Consequence: ENSG00000299545 ENST00000764486.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.401
• Publications: 4 publications found

Genes affected

ENSG00000299545 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.65).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.666 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
ENSG00000299545	ENST00000764486.1	n.67+2142C>T		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.574 AC: 87154 AN: 151898 Hom.: 25518 Cov.: 32

Gnomad AFR AF: 0.672

Gnomad AMI AF: 0.600

Gnomad AMR AF: 0.560

Gnomad ASJ AF: 0.385

Gnomad EAS AF: 0.534

Gnomad SAS AF: 0.660

Gnomad FIN AF: 0.598

Gnomad MID AF: 0.542

Gnomad NFE AF: 0.520

Gnomad OTH AF: 0.549

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

GnomAD4 genome AF: 0.574 AC: 87264 AN: 152016 Hom.: 25572 Cov.: 32 AF XY: 0.578 AC XY: 42964 AN XY: 74314

African (AFR) AF: 0.672 AC: 27882 AN: 41480

American (AMR) AF: 0.560 AC: 8564 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.385 AC: 1334 AN: 3466

East Asian (EAS) AF: 0.535 AC: 2753 AN: 5148

South Asian (SAS) AF: 0.660 AC: 3184 AN: 4822

European-Finnish (FIN) AF: 0.598 AC: 6327 AN: 10574

Middle Eastern (MID) AF: 0.555 AC: 161 AN: 290

European-Non Finnish (NFE) AF: 0.520 AC: 35345 AN: 67930

Other (OTH) AF: 0.554 AC: 1168 AN: 2108

Alfa AF: 0.507 Hom.: 7533

Bravo AF: 0.570

Asia WGS AF: 0.615 AC: 2139 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.65
CADD	Benign	15
DANN	Benign	0.81
PhyloP100		0.40

Splicing

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

Other links and lift over

dbSNP: rs932492; hg19: chr6-80474572;