rs2876711

Positions:

• chr13-76842369-T-C
• chr13-76842369-T-G

Variant summary

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

The ENST00000646457.1(ENSG00000284809):​n.372-4005T>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 0.387 in 151,966 control chromosomes in the GnomAD database, including 12,007 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 0.39 (12007 hom., cov: 31)
• Consequence: ENST00000646457.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.365

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.729 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000646457.1	n.372-4005T>C		intron_variant, non_coding_transcript_variant
	ENST00000648060.1	n.124+4032A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.388 AC: 58847 AN: 151848 Hom.: 12002 Cov.: 31

Gnomad AFR AF: 0.318

Gnomad AMI AF: 0.171

Gnomad AMR AF: 0.409

Gnomad ASJ AF: 0.266

Gnomad EAS AF: 0.748

Gnomad SAS AF: 0.287

Gnomad FIN AF: 0.453

Gnomad MID AF: 0.244

Gnomad NFE AF: 0.405

Gnomad OTH AF: 0.367

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

GnomAD4 genome AF: 0.387 AC: 58875 AN: 151966 Hom.: 12007 Cov.: 31 AF XY: 0.391 AC XY: 29025 AN XY: 74276

Gnomad4 AFR AF: 0.317

Gnomad4 AMR AF: 0.409

Gnomad4 ASJ AF: 0.266

Gnomad4 EAS AF: 0.749

Gnomad4 SAS AF: 0.287

Gnomad4 FIN AF: 0.453

Gnomad4 NFE AF: 0.405

Gnomad4 OTH AF: 0.370

Alfa AF: 0.392 Hom.: 16388

Bravo AF: 0.385

Asia WGS AF: 0.461 AC: 1601 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.2
DANN	Benign	0.81

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2876711; hg19: chr13-77416504;