rs1860300

Variant names:

• chr17-11231370-C-A
• rs1860300
• ENST00000648331.1:n.98+10595G>T

Your query was ambiguous. Multiple possible variants found:

• chr17-11231370-C-A
• chr17-11231370-C-G

Variant summary

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

The ENST00000648331.1(ENSG00000285541):​n.98+10595G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.507 in 151,892 control chromosomes in the GnomAD database, including 20,528 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 0.51 (20528 hom., cov: 32)
• Consequence: ENSG00000285541 ENST00000648331.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.347
• Publications: 8 publications found

Genes affected

ENSG00000285541 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.638 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
ENSG00000285541	ENST00000648331.1	n.98+10595G>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.507 AC: 77023 AN: 151774 Hom.: 20520 Cov.: 32

Gnomad AFR AF: 0.343

Gnomad AMI AF: 0.599

Gnomad AMR AF: 0.649

Gnomad ASJ AF: 0.601

Gnomad EAS AF: 0.410

Gnomad SAS AF: 0.427

Gnomad FIN AF: 0.542

Gnomad MID AF: 0.503

Gnomad NFE AF: 0.577

Gnomad OTH AF: 0.538

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

GnomAD4 genome AF: 0.507 AC: 77057 AN: 151892 Hom.: 20528 Cov.: 32 AF XY: 0.507 AC XY: 37655 AN XY: 74222

African (AFR) AF: 0.343 AC: 14193 AN: 41406

American (AMR) AF: 0.649 AC: 9907 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.601 AC: 2087 AN: 3470

East Asian (EAS) AF: 0.409 AC: 2108 AN: 5150

South Asian (SAS) AF: 0.426 AC: 2051 AN: 4814

European-Finnish (FIN) AF: 0.542 AC: 5701 AN: 10518

Middle Eastern (MID) AF: 0.493 AC: 143 AN: 290

European-Non Finnish (NFE) AF: 0.577 AC: 39185 AN: 67952

Other (OTH) AF: 0.538 AC: 1138 AN: 2114

Alfa AF: 0.536 Hom.: 7453

Bravo AF: 0.510

Asia WGS AF: 0.410 AC: 1424 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	2.8
DANN	Benign	0.35
PhyloP100		-0.35

Splicing

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

Other links and lift over

dbSNP: rs1860300; hg19: chr17-11134687;