rs2186024

Positions:

• chr1-192460955-A-C

Variant summary

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

The ENST00000642855.1(ENSG00000285280):​n.859+15084T>G 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 0.478 in 151,988 control chromosomes in the GnomAD database, including 17,646 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 0.48 (17646 hom., cov: 32)
• Consequence: ENST00000642855.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.13

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.05).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.561 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000642855.1	n.859+15084T>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.478 AC: 72562 AN: 151870 Hom.: 17606 Cov.: 32

Gnomad AFR AF: 0.567

Gnomad AMI AF: 0.311

Gnomad AMR AF: 0.495

Gnomad ASJ AF: 0.497

Gnomad EAS AF: 0.417

Gnomad SAS AF: 0.343

Gnomad FIN AF: 0.409

Gnomad MID AF: 0.443

Gnomad NFE AF: 0.447

Gnomad OTH AF: 0.461

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

GnomAD4 genome AF: 0.478 AC: 72659 AN: 151988 Hom.: 17646 Cov.: 32 AF XY: 0.475 AC XY: 35269 AN XY: 74290

Gnomad4 AFR AF: 0.567

Gnomad4 AMR AF: 0.495

Gnomad4 ASJ AF: 0.497

Gnomad4 EAS AF: 0.418

Gnomad4 SAS AF: 0.344

Gnomad4 FIN AF: 0.409

Gnomad4 NFE AF: 0.447

Gnomad4 OTH AF: 0.464

Alfa AF: 0.451 Hom.: 34028

Bravo AF: 0.492

Asia WGS AF: 0.366 AC: 1275 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.11
DANN	Benign	0.37

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2186024; hg19: chr1-192430085;