13-67750884-T-G

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 1 publications found

Genes affected

ENSG00000287876 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000662515.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000287876	ENST00000662515.1		n.30-21802A>C		intron	N/A

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

African (AFR) AF: 0.186 AC: 7712 AN: 41362

American (AMR) AF: 0.0449 AC: 683 AN: 15226

Ashkenazi Jewish (ASJ) AF: 0.0338 AC: 117 AN: 3464

East Asian (EAS) AF: 0.0173 AC: 89 AN: 5152

South Asian (SAS) AF: 0.129 AC: 623 AN: 4820

European-Finnish (FIN) AF: 0.0141 AC: 150 AN: 10612

Middle Eastern (MID) AF: 0.0204 AC: 6 AN: 294

European-Non Finnish (NFE) AF: 0.0174 AC: 1183 AN: 67924

Other (OTH) AF: 0.0598 AC: 126 AN: 2108

Alfa AF: 0.0453 Hom.: 63

Bravo AF: 0.0757

Asia WGS AF: 0.0640 AC: 222 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.23
DANN	Benign	0.47
PhyloP100		-3.1

Splicing

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

Other links and lift over

dbSNP: rs8002762; hg19: chr13-68325016;