chr15-92263061-G-A

Variant names:

• chr15-92263061-G-A
• rs4304977
• ENST00000561674.1:n.185+49980C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000561674.1(ENSG00000260661):​n.185+49980C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.539 in 152,042 control chromosomes in the GnomAD database, including 23,041 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 0.54 (23041 hom., cov: 33)
• Consequence: ENSG00000260661 ENST00000561674.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.21
• Publications: 0 publications found

Genes affected

ENSG00000260661 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.679 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000260661	ENST00000561674.1	n.185+49980C>T		intron_variant	Intron 2 of 3	1
ENSG00000260661	ENST00000769885.1	n.272+49980C>T		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.538 AC: 81782 AN: 151926 Hom.: 22983 Cov.: 33

Gnomad AFR AF: 0.685

Gnomad AMI AF: 0.510

Gnomad AMR AF: 0.581

Gnomad ASJ AF: 0.577

Gnomad EAS AF: 0.480

Gnomad SAS AF: 0.504

Gnomad FIN AF: 0.355

Gnomad MID AF: 0.595

Gnomad NFE AF: 0.471

Gnomad OTH AF: 0.571

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

GnomAD4 genome AF: 0.539 AC: 81902 AN: 152042 Hom.: 23041 Cov.: 33 AF XY: 0.535 AC XY: 39731 AN XY: 74300

African (AFR) AF: 0.686 AC: 28476 AN: 41506

American (AMR) AF: 0.581 AC: 8882 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.577 AC: 2004 AN: 3472

East Asian (EAS) AF: 0.480 AC: 2478 AN: 5160

South Asian (SAS) AF: 0.504 AC: 2426 AN: 4812

European-Finnish (FIN) AF: 0.355 AC: 3741 AN: 10532

Middle Eastern (MID) AF: 0.592 AC: 174 AN: 294

European-Non Finnish (NFE) AF: 0.472 AC: 32043 AN: 67958

Other (OTH) AF: 0.575 AC: 1214 AN: 2110

Alfa AF: 0.508 Hom.: 22167

Bravo AF: 0.563

Asia WGS AF: 0.557 AC: 1939 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.21
DANN	Benign	0.53
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs4304977; hg19: chr15-92806291;