rs1910003

chr5-125968854-G-A

Variant summary

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

The ENST00000651847.1(ENSG00000248752):n.471+8666C>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 0.12 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: ENST00000651847.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.466

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC124901056	XR_007058919.1	n.1774+129153C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000651847.1	n.471+8666C>T		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.133

Gnomad4 AMR AF: 0.0801

Gnomad4 ASJ AF: 0.110

Gnomad4 EAS AF: 0.110

Gnomad4 SAS AF: 0.133

Gnomad4 FIN AF: 0.120

Gnomad4 NFE AF: 0.122

Gnomad4 OTH AF: 0.114

Alfa AF: 0.119 Hom.: 2225

Bravo AF: 0.117

Asia WGS AF: 0.104 AC: 361 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	8.2
Dann	Benign	0.38

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1910003; hg19: chr5-125304547; COSMIC: COSV72115551;