rs10061706

Variant names:

• chr5-105074083-C-T
• rs10061706
• ENST00000503650.1:n.211-187108G>A

Variant summary

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

The ENST00000503650.1(ENSG00000251574):​n.211-187108G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.629 in 152,008 control chromosomes in the GnomAD database, including 31,983 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 0.63 (31983 hom., cov: 32)
• Consequence: ENSG00000251574 ENST00000503650.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.381
• Publications: 4 publications found

Genes affected

ENSG00000251574 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.736 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
ENSG00000251574	ENST00000503650.1	n.211-187108G>A		intron_variant	Intron 1 of 2	3
ENSG00000251574	ENST00000522464.1	n.69-65172G>A		intron_variant	Intron 1 of 4	3
ENSG00000251574	ENST00000718095.1	n.211-65172G>A		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.629 AC: 95535 AN: 151888 Hom.: 31971 Cov.: 32

Gnomad AFR AF: 0.427

Gnomad AMI AF: 0.886

Gnomad AMR AF: 0.636

Gnomad ASJ AF: 0.740

Gnomad EAS AF: 0.269

Gnomad SAS AF: 0.645

Gnomad FIN AF: 0.795

Gnomad MID AF: 0.627

Gnomad NFE AF: 0.741

Gnomad OTH AF: 0.647

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

GnomAD4 genome AF: 0.629 AC: 95575 AN: 152008 Hom.: 31983 Cov.: 32 AF XY: 0.630 AC XY: 46843 AN XY: 74298

African (AFR) AF: 0.426 AC: 17677 AN: 41454

American (AMR) AF: 0.636 AC: 9717 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.740 AC: 2565 AN: 3468

East Asian (EAS) AF: 0.268 AC: 1380 AN: 5146

South Asian (SAS) AF: 0.645 AC: 3101 AN: 4808

European-Finnish (FIN) AF: 0.795 AC: 8409 AN: 10572

Middle Eastern (MID) AF: 0.630 AC: 184 AN: 292

European-Non Finnish (NFE) AF: 0.741 AC: 50373 AN: 67972

Other (OTH) AF: 0.644 AC: 1361 AN: 2112

Alfa AF: 0.710 Hom.: 21830

Bravo AF: 0.604

Asia WGS AF: 0.484 AC: 1684 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	5.8
DANN	Benign	0.45
PhyloP100		-0.38

Splicing

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

Other links and lift over

dbSNP: rs10061706; hg19: chr5-104409784;