15-61410580-A-G

Position:

• chr15-61410580-A-G

Variant summary

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

The ENST00000559783.2(ENSG00000259616):​n.187-10149T>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 0.837 in 152,220 control chromosomes in the GnomAD database, including 54,504 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 0.84 (54504 hom., cov: 34)
• Consequence: ENST00000559783.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.764

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.909 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105370847	XR_932332.2	n.251-136A>G		intron_variant, non_coding_transcript_variant
LOC105370847	XR_932333.2	n.251-136A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000559783.2	n.187-10149T>C		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.837 AC: 127381 AN: 152102 Hom.: 54468 Cov.: 34

Gnomad AFR AF: 0.826

Gnomad AMI AF: 0.911

Gnomad AMR AF: 0.669

Gnomad ASJ AF: 0.869

Gnomad EAS AF: 0.379

Gnomad SAS AF: 0.779

Gnomad FIN AF: 0.862

Gnomad MID AF: 0.924

Gnomad NFE AF: 0.915

Gnomad OTH AF: 0.836

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

GnomAD4 genome AF: 0.837 AC: 127461 AN: 152220 Hom.: 54504 Cov.: 34 AF XY: 0.827 AC XY: 61569 AN XY: 74406

Gnomad4 AFR AF: 0.826

Gnomad4 AMR AF: 0.668

Gnomad4 ASJ AF: 0.869

Gnomad4 EAS AF: 0.379

Gnomad4 SAS AF: 0.781

Gnomad4 FIN AF: 0.862

Gnomad4 NFE AF: 0.915

Gnomad4 OTH AF: 0.831

Alfa AF: 0.890 Hom.: 123717

Bravo AF: 0.816

Asia WGS AF: 0.582 AC: 2027 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.20
DANN	Benign	0.73

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3884558; hg19: chr15-61702779;