rs679090

Positions:

• chr13-76973656-C-T

Variant summary

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

The XR_001749929.1(LOC105370269):​n.212+2860G>A 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 0.781 in 152,112 control chromosomes in the GnomAD database, including 46,981 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 0.78 (46981 hom., cov: 32)
• Consequence: LOC105370269 XR_001749929.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.211

Genes affected

LOC105370269 (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 (NFE) allele frequency at 95% confidence interval = 0.82 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105370269	XR_001749929.1	n.212+2860G>A		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.781 AC: 118676 AN: 151994 Hom.: 46958 Cov.: 32

Gnomad AFR AF: 0.780

Gnomad AMI AF: 0.788

Gnomad AMR AF: 0.772

Gnomad ASJ AF: 0.836

Gnomad EAS AF: 0.471

Gnomad SAS AF: 0.515

Gnomad FIN AF: 0.759

Gnomad MID AF: 0.826

Gnomad NFE AF: 0.826

Gnomad OTH AF: 0.792

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

GnomAD4 genome AF: 0.781 AC: 118746 AN: 152112 Hom.: 46981 Cov.: 32 AF XY: 0.770 AC XY: 57227 AN XY: 74342

Gnomad4 AFR AF: 0.780

Gnomad4 AMR AF: 0.772

Gnomad4 ASJ AF: 0.836

Gnomad4 EAS AF: 0.470

Gnomad4 SAS AF: 0.516

Gnomad4 FIN AF: 0.759

Gnomad4 NFE AF: 0.826

Gnomad4 OTH AF: 0.789

Alfa AF: 0.808 Hom.: 64641

Bravo AF: 0.785

Asia WGS AF: 0.486 AC: 1692 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	5.6
DANN	Benign	0.76

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs679090; hg19: chr13-77547791;