rs10061706

chr5-105074083-C-T

Variant summary

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

The ENST00000503650.1(ENSG00000251574):n.211-187108G>A 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 0.629 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: ENST00000503650.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.381

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000503650.1	n.211-187108G>A		intron_variant, non_coding_transcript_variant		3
	ENST00000522464.1	n.69-65172G>A		intron_variant, non_coding_transcript_variant		3

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

Gnomad4 AFR AF: 0.426

Gnomad4 AMR AF: 0.636

Gnomad4 ASJ AF: 0.740

Gnomad4 EAS AF: 0.268

Gnomad4 SAS AF: 0.645

Gnomad4 FIN AF: 0.795

Gnomad4 NFE AF: 0.741

Gnomad4 OTH AF: 0.644

Alfa AF: 0.711 Hom.: 19705

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10061706; hg19: chr5-104409784;