rs10518669

Positions:

• chr1-82634035-G-A

Variant summary

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

The ENST00000650063.1(ENSG00000233290):​n.474+21981C>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 0.116 in 152,078 control chromosomes in the GnomAD database, including 1,330 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 0.12 (1330 hom., cov: 32)
• Consequence: ENST00000650063.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0120

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.199 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105378814	XR_947533.2	n.503-1920G>A		intron_variant, non_coding_transcript_variant
LOC105378814	XR_947532.3	n.503-1920G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000650063.1	n.474+21981C>T		intron_variant, non_coding_transcript_variant
	ENST00000653483.1	n.306+21981C>T		intron_variant, non_coding_transcript_variant
	ENST00000663002.1	n.166+21981C>T		intron_variant, non_coding_transcript_variant
	ENST00000702694.1	n.166+21981C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.116 AC: 17654 AN: 151960 Hom.: 1322 Cov.: 32

Gnomad AFR AF: 0.203

Gnomad AMI AF: 0.111

Gnomad AMR AF: 0.105

Gnomad ASJ AF: 0.0696

Gnomad EAS AF: 0.0714

Gnomad SAS AF: 0.150

Gnomad FIN AF: 0.142

Gnomad MID AF: 0.127

Gnomad NFE AF: 0.0661

Gnomad OTH AF: 0.100

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

GnomAD4 genome AF: 0.116 AC: 17688 AN: 152078 Hom.: 1330 Cov.: 32 AF XY: 0.121 AC XY: 8964 AN XY: 74360

Gnomad4 AFR AF: 0.203

Gnomad4 AMR AF: 0.105

Gnomad4 ASJ AF: 0.0696

Gnomad4 EAS AF: 0.0713

Gnomad4 SAS AF: 0.151

Gnomad4 FIN AF: 0.142

Gnomad4 NFE AF: 0.0661

Gnomad4 OTH AF: 0.102

Alfa AF: 0.103 Hom.: 133

Bravo AF: 0.116

Asia WGS AF: 0.107 AC: 370 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.73
DANN	Benign	0.19

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10518669; hg19: chr1-83099718;