rs1377185

chr1-214947010-C-T

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000658732.1(ENSG00000287008):n.102C>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.182 in 152,110 control chromosomes in the GnomAD database, including 2,689 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 0.18 (2689 hom., cov: 32)
• Consequence: ENST00000658732.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0130

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.45).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.285 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
	ENST00000658732.1	n.102C>T		non_coding_transcript_exon_variant	1/2

Frequencies

GnomAD3 genomes AF: 0.182 AC: 27652 AN: 151992 Hom.: 2678 Cov.: 32

Gnomad AFR AF: 0.235

Gnomad AMI AF: 0.0625

Gnomad AMR AF: 0.174

Gnomad ASJ AF: 0.189

Gnomad EAS AF: 0.297

Gnomad SAS AF: 0.215

Gnomad FIN AF: 0.104

Gnomad MID AF: 0.256

Gnomad NFE AF: 0.153

Gnomad OTH AF: 0.202

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

GnomAD4 genome AF: 0.182 AC: 27689 AN: 152110 Hom.: 2689 Cov.: 32 AF XY: 0.180 AC XY: 13381 AN XY: 74342

Gnomad4 AFR AF: 0.235

Gnomad4 AMR AF: 0.174

Gnomad4 ASJ AF: 0.189

Gnomad4 EAS AF: 0.298

Gnomad4 SAS AF: 0.217

Gnomad4 FIN AF: 0.104

Gnomad4 NFE AF: 0.153

Gnomad4 OTH AF: 0.201

Alfa AF: 0.166 Hom.: 1351

Bravo AF: 0.190

Asia WGS AF: 0.269 AC: 932 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.45
Cadd	Benign	8.5
Dann	Benign	0.70

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1377185; hg19: chr1-215120353;