13-67750884-T-G

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, non coding transcript 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: ENST00000662515.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.13

Genes affected

(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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000662515.1	n.30-21802A>C		intron_variant, non_coding_transcript_variant

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;