rs1860190

Variant names:

• chr17-34249554-T-A
• rs1860190
• ENST00000776537.1:n.238+2319A>T

Your query was ambiguous. Multiple possible variants found:

• chr17-34249554-T-A
• chr17-34249554-T-G

Variant summary

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

The ENST00000776537.1(ENSG00000301139):​n.238+2319A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.473 in 152,160 control chromosomes in the GnomAD database, including 18,427 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 0.47 (18427 hom., cov: 33)
• Consequence: ENSG00000301139 ENST00000776537.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0340
• Publications: 15 publications found

Genes affected

ENSG00000301139 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.659 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
ENSG00000301139	ENST00000776537.1	n.238+2319A>T		intron_variant	Intron 2 of 2
ENSG00000301139	ENST00000776538.1	n.238+2319A>T		intron_variant	Intron 2 of 2
ENSG00000301139	ENST00000776539.1	n.236+2319A>T		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.473 AC: 71914 AN: 152042 Hom.: 18386 Cov.: 33

Gnomad AFR AF: 0.666

Gnomad AMI AF: 0.222

Gnomad AMR AF: 0.541

Gnomad ASJ AF: 0.335

Gnomad EAS AF: 0.559

Gnomad SAS AF: 0.445

Gnomad FIN AF: 0.405

Gnomad MID AF: 0.459

Gnomad NFE AF: 0.357

Gnomad OTH AF: 0.457

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

GnomAD4 genome AF: 0.473 AC: 72008 AN: 152160 Hom.: 18427 Cov.: 33 AF XY: 0.476 AC XY: 35444 AN XY: 74386

African (AFR) AF: 0.666 AC: 27639 AN: 41530

American (AMR) AF: 0.542 AC: 8291 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.335 AC: 1163 AN: 3468

East Asian (EAS) AF: 0.559 AC: 2897 AN: 5178

South Asian (SAS) AF: 0.446 AC: 2155 AN: 4828

European-Finnish (FIN) AF: 0.405 AC: 4287 AN: 10574

Middle Eastern (MID) AF: 0.446 AC: 131 AN: 294

European-Non Finnish (NFE) AF: 0.357 AC: 24285 AN: 67978

Other (OTH) AF: 0.454 AC: 958 AN: 2108

Alfa AF: 0.413 Hom.: 1732

Bravo AF: 0.492

Asia WGS AF: 0.506 AC: 1758 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.9
DANN	Benign	0.82
PhyloP100		-0.034

Splicing

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

Other links and lift over

dbSNP: rs1860190; hg19: chr17-32576573;