1-82846152-C-T

Variant names:

• chr1-82846152-C-T
• rs11163585
• ENST00000650063.1:n.62+1992G>A

Variant summary

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

The ENST00000650063.1(ENSG00000233290):​n.62+1992G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.247 in 151,942 control chromosomes in the GnomAD database, including 4,944 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 0.25 (4944 hom., cov: 32)
• Consequence: ENSG00000233290 ENST00000650063.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00800
• Publications: 14 publications found

Genes affected

ENSG00000233290 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.287 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
ENSG00000233290	ENST00000650063.1	n.62+1992G>A		intron_variant	Intron 1 of 6
ENSG00000233290	ENST00000834557.1	n.91+1992G>A		intron_variant	Intron 1 of 2
ENSG00000233290	ENST00000834566.1	n.62+1992G>A		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.247 AC: 37450 AN: 151824 Hom.: 4937 Cov.: 32

Gnomad AFR AF: 0.220

Gnomad AMI AF: 0.284

Gnomad AMR AF: 0.219

Gnomad ASJ AF: 0.308

Gnomad EAS AF: 0.0390

Gnomad SAS AF: 0.283

Gnomad FIN AF: 0.171

Gnomad MID AF: 0.271

Gnomad NFE AF: 0.290

Gnomad OTH AF: 0.255

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

GnomAD4 genome AF: 0.247 AC: 37483 AN: 151942 Hom.: 4944 Cov.: 32 AF XY: 0.242 AC XY: 17965 AN XY: 74288

African (AFR) AF: 0.220 AC: 9119 AN: 41434

American (AMR) AF: 0.220 AC: 3343 AN: 15228

Ashkenazi Jewish (ASJ) AF: 0.308 AC: 1069 AN: 3468

East Asian (EAS) AF: 0.0387 AC: 200 AN: 5164

South Asian (SAS) AF: 0.284 AC: 1369 AN: 4824

European-Finnish (FIN) AF: 0.171 AC: 1808 AN: 10562

Middle Eastern (MID) AF: 0.274 AC: 80 AN: 292

European-Non Finnish (NFE) AF: 0.290 AC: 19701 AN: 67948

Other (OTH) AF: 0.254 AC: 535 AN: 2110

Alfa AF: 0.274 Hom.: 18334

Bravo AF: 0.246

Asia WGS AF: 0.159 AC: 554 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	6.6
DANN	Benign	0.53
PhyloP100		0.0080

Splicing

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

Other links and lift over

dbSNP: rs11163585; hg19: chr1-83311835;