rs1010824

Variant names:

• chr8-107239685-G-A
• rs1010824
• ENST00000801168.1:n.196+918C>T

Variant summary

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

The ENST00000801168.1(ENSG00000304228):​n.196+918C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.147 in 151,778 control chromosomes in the GnomAD database, including 2,076 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 0.15 (2076 hom., cov: 31)
• Consequence: ENSG00000304228 ENST00000801168.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.59
• Publications: 10 publications found

Genes affected

ENSG00000304228 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.302 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
ENSG00000304228	ENST00000801168.1	n.196+918C>T		intron_variant	Intron 2 of 2
ENSG00000304228	ENST00000801169.1	n.383+918C>T		intron_variant	Intron 1 of 1
ENSG00000304228	ENST00000801170.1	n.175+918C>T		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.147 AC: 22260 AN: 151662 Hom.: 2080 Cov.: 31

Gnomad AFR AF: 0.0443

Gnomad AMI AF: 0.151

Gnomad AMR AF: 0.207

Gnomad ASJ AF: 0.115

Gnomad EAS AF: 0.314

Gnomad SAS AF: 0.168

Gnomad FIN AF: 0.238

Gnomad MID AF: 0.0759

Gnomad NFE AF: 0.169

Gnomad OTH AF: 0.160

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

GnomAD4 genome AF: 0.147 AC: 22258 AN: 151778 Hom.: 2076 Cov.: 31 AF XY: 0.153 AC XY: 11360 AN XY: 74138

African (AFR) AF: 0.0442 AC: 1829 AN: 41366

American (AMR) AF: 0.206 AC: 3140 AN: 15240

Ashkenazi Jewish (ASJ) AF: 0.115 AC: 399 AN: 3466

East Asian (EAS) AF: 0.315 AC: 1610 AN: 5112

South Asian (SAS) AF: 0.169 AC: 811 AN: 4812

European-Finnish (FIN) AF: 0.238 AC: 2501 AN: 10502

Middle Eastern (MID) AF: 0.0680 AC: 20 AN: 294

European-Non Finnish (NFE) AF: 0.169 AC: 11472 AN: 67964

Other (OTH) AF: 0.160 AC: 338 AN: 2110

Alfa AF: 0.160 Hom.: 752

Bravo AF: 0.140

Asia WGS AF: 0.251 AC: 871 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.042
DANN	Benign	0.73
PhyloP100		-1.6

Splicing

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

Other links and lift over

dbSNP: rs1010824; hg19: chr8-108251913;