rs1860300

chr17-11231370-C-Achr17-11231370-C-G

Variant summary

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

The ENST00000648331.1(ENSG00000285541):n.98+10595G>T 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 0.507 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: ENST00000648331.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.347

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000648331.1	n.98+10595G>T		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.343

Gnomad4 AMR AF: 0.649

Gnomad4 ASJ AF: 0.601

Gnomad4 EAS AF: 0.409

Gnomad4 SAS AF: 0.426

Gnomad4 FIN AF: 0.542

Gnomad4 NFE AF: 0.577

Gnomad4 OTH AF: 0.538

Alfa AF: 0.541 Hom.: 3743

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1860300; hg19: chr17-11134687;