rs10493450

Positions:

• chr1-68807756-A-T

Variant summary

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

The ENST00000643361.1(ENSG00000285407):​n.419-56068A>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 0.13 in 152,156 control chromosomes in the GnomAD database, including 1,505 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 0.13 (1505 hom., cov: 32)
• Consequence: ENST00000643361.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0950

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.185 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000643361.1	n.419-56068A>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.130 AC: 19699 AN: 152038 Hom.: 1502 Cov.: 32

Gnomad AFR AF: 0.176

Gnomad AMI AF: 0.0954

Gnomad AMR AF: 0.191

Gnomad ASJ AF: 0.139

Gnomad EAS AF: 0.0472

Gnomad SAS AF: 0.0626

Gnomad FIN AF: 0.0856

Gnomad MID AF: 0.120

Gnomad NFE AF: 0.105

Gnomad OTH AF: 0.139

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

GnomAD4 genome AF: 0.130 AC: 19721 AN: 152156 Hom.: 1505 Cov.: 32 AF XY: 0.126 AC XY: 9355 AN XY: 74396

Gnomad4 AFR AF: 0.176

Gnomad4 AMR AF: 0.191

Gnomad4 ASJ AF: 0.139

Gnomad4 EAS AF: 0.0470

Gnomad4 SAS AF: 0.0627

Gnomad4 FIN AF: 0.0856

Gnomad4 NFE AF: 0.105

Gnomad4 OTH AF: 0.137

Alfa AF: 0.124 Hom.: 191

Bravo AF: 0.144

Asia WGS AF: 0.0670 AC: 233 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	4.2
DANN	Benign	0.64

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10493450; hg19: chr1-69273439;