chr1-162458485-T-C

Variant names:

• chr1-162458485-T-C
• rs10800559
• ENST00000832888.1:n.258+8824A>G

Variant summary

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

The ENST00000832888.1(ENSG00000308263):​n.258+8824A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.191 in 152,136 control chromosomes in the GnomAD database, including 3,505 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 0.19 (3505 hom., cov: 32)
• Consequence: ENSG00000308263 ENST00000832888.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.192
• Publications: 10 publications found

Genes affected

ENSG00000308263 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.7).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.432 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
ENSG00000308263	ENST00000832888.1	n.258+8824A>G		intron_variant	Intron 2 of 2
ENSG00000308263	ENST00000832889.1	n.229-6783A>G		intron_variant	Intron 1 of 1
ENSG00000308263	ENST00000832890.1	n.471+6693A>G		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.191 AC: 29052 AN: 152018 Hom.: 3499 Cov.: 32

Gnomad AFR AF: 0.0473

Gnomad AMI AF: 0.188

Gnomad AMR AF: 0.265

Gnomad ASJ AF: 0.173

Gnomad EAS AF: 0.447

Gnomad SAS AF: 0.274

Gnomad FIN AF: 0.274

Gnomad MID AF: 0.168

Gnomad NFE AF: 0.225

Gnomad OTH AF: 0.185

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

GnomAD4 genome AF: 0.191 AC: 29063 AN: 152136 Hom.: 3505 Cov.: 32 AF XY: 0.199 AC XY: 14815 AN XY: 74362

African (AFR) AF: 0.0472 AC: 1961 AN: 41572

American (AMR) AF: 0.265 AC: 4052 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.173 AC: 602 AN: 3472

East Asian (EAS) AF: 0.447 AC: 2308 AN: 5158

South Asian (SAS) AF: 0.273 AC: 1317 AN: 4818

European-Finnish (FIN) AF: 0.274 AC: 2892 AN: 10552

Middle Eastern (MID) AF: 0.177 AC: 52 AN: 294

European-Non Finnish (NFE) AF: 0.225 AC: 15322 AN: 67980

Other (OTH) AF: 0.183 AC: 386 AN: 2108

Alfa AF: 0.218 Hom.: 7832

Bravo AF: 0.185

Asia WGS AF: 0.336 AC: 1170 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.70
CADD	Benign	10
DANN	Benign	0.89
PhyloP100		0.19

Splicing

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

Other links and lift over

dbSNP: rs10800559; hg19: chr1-162428275;