5-62689026-A-G

Variant names:

• chr5-62689026-A-G
• rs1423386
• ENST00000760975.1:n.68-8798T>C

Variant summary

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

The ENST00000760975.1(ENSG00000299141):​n.68-8798T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.189 in 152,152 control chromosomes in the GnomAD database, including 2,887 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 0.19 (2887 hom., cov: 31)
• Consequence: ENSG00000299141 ENST00000760975.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.444
• Publications: 7 publications found

Genes affected

ENSG00000299141 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.308 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000299141	ENST00000760975.1	n.68-8798T>C		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.189 AC: 28780 AN: 152034 Hom.: 2877 Cov.: 31

Gnomad AFR AF: 0.208

Gnomad AMI AF: 0.304

Gnomad AMR AF: 0.151

Gnomad ASJ AF: 0.236

Gnomad EAS AF: 0.320

Gnomad SAS AF: 0.150

Gnomad FIN AF: 0.139

Gnomad MID AF: 0.184

Gnomad NFE AF: 0.183

Gnomad OTH AF: 0.183

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

GnomAD4 genome AF: 0.189 AC: 28820 AN: 152152 Hom.: 2887 Cov.: 31 AF XY: 0.186 AC XY: 13873 AN XY: 74390

African (AFR) AF: 0.208 AC: 8645 AN: 41510

American (AMR) AF: 0.151 AC: 2313 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.236 AC: 820 AN: 3468

East Asian (EAS) AF: 0.321 AC: 1657 AN: 5170

South Asian (SAS) AF: 0.151 AC: 727 AN: 4824

European-Finnish (FIN) AF: 0.139 AC: 1467 AN: 10592

Middle Eastern (MID) AF: 0.190 AC: 56 AN: 294

European-Non Finnish (NFE) AF: 0.183 AC: 12474 AN: 67994

Other (OTH) AF: 0.182 AC: 384 AN: 2112

Alfa AF: 0.189 Hom.: 5573

Bravo AF: 0.194

Asia WGS AF: 0.219 AC: 759 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.74
DANN	Benign	0.55
PhyloP100		-0.44

Splicing

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

Other links and lift over

dbSNP: rs1423386; hg19: chr5-61984853;