13-76715842-A-G

Position:

• chr13-76715842-A-G

Variant summary

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

The ENST00000648060.1(ENSG00000285572):​n.395+13503T>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 0.333 in 151,400 control chromosomes in the GnomAD database, including 10,605 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 0.33 (10605 hom., cov: 30)
• Consequence: ENST00000648060.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.15

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.532 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105370265	XR_001749923.2	n.284-1084T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000648060.1	n.395+13503T>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.334 AC: 50483 AN: 151280 Hom.: 10599 Cov.: 30

Gnomad AFR AF: 0.0818

Gnomad AMI AF: 0.541

Gnomad AMR AF: 0.541

Gnomad ASJ AF: 0.421

Gnomad EAS AF: 0.477

Gnomad SAS AF: 0.379

Gnomad FIN AF: 0.390

Gnomad MID AF: 0.392

Gnomad NFE AF: 0.410

Gnomad OTH AF: 0.342

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

GnomAD4 genome AF: 0.333 AC: 50485 AN: 151400 Hom.: 10605 Cov.: 30 AF XY: 0.338 AC XY: 24957 AN XY: 73938

Gnomad4 AFR AF: 0.0815

Gnomad4 AMR AF: 0.542

Gnomad4 ASJ AF: 0.421

Gnomad4 EAS AF: 0.478

Gnomad4 SAS AF: 0.379

Gnomad4 FIN AF: 0.390

Gnomad4 NFE AF: 0.410

Gnomad4 OTH AF: 0.338

Alfa AF: 0.406 Hom.: 17413

Bravo AF: 0.336

Asia WGS AF: 0.371 AC: 1293 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.027
DANN	Benign	0.58

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2149698; hg19: chr13-77289977;