13-67750884-T-G

Variant names:

• chr13-67750884-T-G
• rs8002762
• ENST00000662515.1:n.30-21802A>C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000662515.1(ENSG00000287876):​n.30-21802A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0704 in 151,872 control chromosomes in the GnomAD database, including 869 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 0.070 (869 hom., cov: 32)
• Consequence: ENSG00000287876 ENST00000662515.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.13

Genes affected

ENSG00000287876 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.183 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
ENSG00000287876	ENST00000662515.1	n.30-21802A>C		intron_variant	Intron 1 of 4

Frequencies

GnomAD3 genomes AF: 0.0704 AC: 10682 AN: 151754 Hom.: 871 Cov.: 32

Gnomad AFR AF: 0.187

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0449

Gnomad ASJ AF: 0.0338

Gnomad EAS AF: 0.0172

Gnomad SAS AF: 0.129

Gnomad FIN AF: 0.0141

Gnomad MID AF: 0.0253

Gnomad NFE AF: 0.0175

Gnomad OTH AF: 0.0604

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

GnomAD4 genome AF: 0.0704 AC: 10689 AN: 151872 Hom.: 869 Cov.: 32 AF XY: 0.0705 AC XY: 5237 AN XY: 74258

Gnomad4 AFR AF: 0.186

Gnomad4 AMR AF: 0.0449

Gnomad4 ASJ AF: 0.0338

Gnomad4 EAS AF: 0.0173

Gnomad4 SAS AF: 0.129

Gnomad4 FIN AF: 0.0141

Gnomad4 NFE AF: 0.0174

Gnomad4 OTH AF: 0.0598

Alfa AF: 0.0402 Hom.: 52

Bravo AF: 0.0757

Asia WGS AF: 0.0640 AC: 222 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.23
DANN	Benign	0.47

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs8002762; hg19: chr13-68325016;