rs1910003

Variant names:

• chr5-125968854-G-A
• rs1910003
• ENST00000651847.1:n.471+8666C>T

Your query was ambiguous. Multiple possible variants found:

• chr5-125968854-G-A
• chr5-125968854-G-C
• chr5-125968854-G-T

Variant summary

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

The ENST00000651847.1(ENSG00000248752):​n.471+8666C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.12 in 151,940 control chromosomes in the GnomAD database, including 1,121 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 0.12 (1121 hom., cov: 32)
• Consequence: ENSG00000248752 ENST00000651847.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.466
• Publications: 2 publications found

Genes affected

ENSG00000248752 (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 (SAS) allele frequency at 95% confidence interval = 0.13 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000651847.1. 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
	ENSG00000248752	ENST00000651847.1		n.471+8666C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.120 AC: 18256 AN: 151822 Hom.: 1120 Cov.: 32

Gnomad AFR AF: 0.133

Gnomad AMI AF: 0.113

Gnomad AMR AF: 0.0802

Gnomad ASJ AF: 0.110

Gnomad EAS AF: 0.110

Gnomad SAS AF: 0.133

Gnomad FIN AF: 0.120

Gnomad MID AF: 0.117

Gnomad NFE AF: 0.122

Gnomad OTH AF: 0.115

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

GnomAD4 genome AF: 0.120 AC: 18269 AN: 151940 Hom.: 1121 Cov.: 32 AF XY: 0.119 AC XY: 8872 AN XY: 74250

African (AFR) AF: 0.133 AC: 5508 AN: 41478

American (AMR) AF: 0.0801 AC: 1222 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.110 AC: 383 AN: 3468

East Asian (EAS) AF: 0.110 AC: 561 AN: 5104

South Asian (SAS) AF: 0.133 AC: 641 AN: 4814

European-Finnish (FIN) AF: 0.120 AC: 1264 AN: 10572

Middle Eastern (MID) AF: 0.105 AC: 31 AN: 294

European-Non Finnish (NFE) AF: 0.122 AC: 8314 AN: 67934

Other (OTH) AF: 0.114 AC: 242 AN: 2114

Alfa AF: 0.120 Hom.: 4978

Bravo AF: 0.117

Asia WGS AF: 0.104 AC: 361 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	8.2
DANN	Benign	0.38
PhyloP100		0.47

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: rs1910003;

hg19: chr5-125304547;

COSMIC: COSV72115551;