rs1010254

Variant names:

• chr5-152354548-C-T
• rs1010254
• ENST00000812688.1:n.183+16685C>T

Variant summary

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

The ENST00000812688.1(ENSG00000286749):​n.183+16685C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.34 in 151,944 control chromosomes in the GnomAD database, including 9,603 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 0.34 (9603 hom., cov: 32)
• Consequence: ENSG00000286749 ENST00000812688.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.238
• Publications: 14 publications found

Genes affected

ENSG00000286749 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.495 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000812688.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000286749	ENST00000812688.1		n.183+16685C>T		intron	N/A
	ENSG00000286749	ENST00000812689.1		n.172+16685C>T		intron	N/A
	ENSG00000286749	ENST00000812690.1		n.145-11244C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.340 AC: 51585 AN: 151826 Hom.: 9581 Cov.: 32

Gnomad AFR AF: 0.500

Gnomad AMI AF: 0.277

Gnomad AMR AF: 0.351

Gnomad ASJ AF: 0.296

Gnomad EAS AF: 0.183

Gnomad SAS AF: 0.359

Gnomad FIN AF: 0.266

Gnomad MID AF: 0.415

Gnomad NFE AF: 0.265

Gnomad OTH AF: 0.336

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

GnomAD4 genome AF: 0.340 AC: 51649 AN: 151944 Hom.: 9603 Cov.: 32 AF XY: 0.339 AC XY: 25150 AN XY: 74280

African (AFR) AF: 0.500 AC: 20715 AN: 41394

American (AMR) AF: 0.351 AC: 5366 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.296 AC: 1026 AN: 3466

East Asian (EAS) AF: 0.184 AC: 952 AN: 5168

South Asian (SAS) AF: 0.358 AC: 1721 AN: 4806

European-Finnish (FIN) AF: 0.266 AC: 2806 AN: 10566

Middle Eastern (MID) AF: 0.401 AC: 118 AN: 294

European-Non Finnish (NFE) AF: 0.265 AC: 17985 AN: 67952

Other (OTH) AF: 0.335 AC: 707 AN: 2110

Alfa AF: 0.291 Hom.: 20420

Bravo AF: 0.354

Asia WGS AF: 0.322 AC: 1122 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.98
DANN	Benign	0.75
PhyloP100		-0.24

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs1010254;

hg19: chr5-151734109;