5-122582513-G-T

Variant names:

• chr5-122582513-G-T
• rs7712513
• ENST00000845986.1:n.251G>T

Variant summary

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

The ENST00000845986.1(ENSG00000309921):​n.251G>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 0.71 in 152,114 control chromosomes in the GnomAD database, including 38,493 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 0.71 (38493 hom., cov: 32)
• Consequence: ENSG00000309921 ENST00000845986.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.80
• Publications: 5 publications found

Genes affected

ENSG00000309921 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.773 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC101927357	NR_134281.1	n.2088C>A		non_coding_transcript_exon_variant	Exon 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000309921	ENST00000845986.1	n.251G>T		non_coding_transcript_exon_variant	Exon 2 of 2
ENSG00000309921	ENST00000845985.1	n.48-248G>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.709 AC: 107820 AN: 151996 Hom.: 38424 Cov.: 32

Gnomad AFR AF: 0.776

Gnomad AMI AF: 0.777

Gnomad AMR AF: 0.695

Gnomad ASJ AF: 0.703

Gnomad EAS AF: 0.793

Gnomad SAS AF: 0.735

Gnomad FIN AF: 0.681

Gnomad MID AF: 0.772

Gnomad NFE AF: 0.668

Gnomad OTH AF: 0.696

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

GnomAD4 genome AF: 0.710 AC: 107949 AN: 152114 Hom.: 38493 Cov.: 32 AF XY: 0.712 AC XY: 52898 AN XY: 74334

African (AFR) AF: 0.776 AC: 32222 AN: 41516

American (AMR) AF: 0.695 AC: 10628 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.703 AC: 2440 AN: 3470

East Asian (EAS) AF: 0.793 AC: 4106 AN: 5176

South Asian (SAS) AF: 0.735 AC: 3536 AN: 4812

European-Finnish (FIN) AF: 0.681 AC: 7194 AN: 10564

Middle Eastern (MID) AF: 0.772 AC: 227 AN: 294

European-Non Finnish (NFE) AF: 0.668 AC: 45413 AN: 67974

Other (OTH) AF: 0.698 AC: 1474 AN: 2112

Alfa AF: 0.684 Hom.: 12201

Bravo AF: 0.711

Asia WGS AF: 0.776 AC: 2694 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.0070
DANN	Benign	0.75
PhyloP100		-1.8

Splicing

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

Other links and lift over

dbSNP: rs7712513; hg19: chr5-121918208; COSMIC: COSV60191295;