rs10102377

Variant names:

• chr8-82850587-C-T
• rs10102377
• ENST00000658531.1:n.254-53068C>T

Variant summary

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

The ENST00000658531.1(ENSG00000254394):​n.254-53068C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.228 in 152,008 control chromosomes in the GnomAD database, including 4,086 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 0.23 (4086 hom., cov: 32)
• Consequence: ENSG00000254394 ENST00000658531.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.800
• Publications: 5 publications found

Genes affected

ENSG00000254394 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (SAS) 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
ENSG00000254394	ENST00000658531.1	n.254-53068C>T		intron_variant	Intron 3 of 3
ENSG00000254394	ENST00000663058.1	n.944-62352C>T		intron_variant	Intron 6 of 7

Frequencies

GnomAD3 genomes AF: 0.228 AC: 34592 AN: 151890 Hom.: 4083 Cov.: 32

Gnomad AFR AF: 0.178

Gnomad AMI AF: 0.389

Gnomad AMR AF: 0.254

Gnomad ASJ AF: 0.267

Gnomad EAS AF: 0.224

Gnomad SAS AF: 0.301

Gnomad FIN AF: 0.222

Gnomad MID AF: 0.340

Gnomad NFE AF: 0.243

Gnomad OTH AF: 0.225

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

GnomAD4 genome AF: 0.228 AC: 34618 AN: 152008 Hom.: 4086 Cov.: 32 AF XY: 0.228 AC XY: 16942 AN XY: 74262

African (AFR) AF: 0.178 AC: 7381 AN: 41464

American (AMR) AF: 0.255 AC: 3888 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.267 AC: 926 AN: 3468

East Asian (EAS) AF: 0.225 AC: 1161 AN: 5162

South Asian (SAS) AF: 0.300 AC: 1446 AN: 4816

European-Finnish (FIN) AF: 0.222 AC: 2344 AN: 10560

Middle Eastern (MID) AF: 0.355 AC: 103 AN: 290

European-Non Finnish (NFE) AF: 0.243 AC: 16537 AN: 67958

Other (OTH) AF: 0.226 AC: 477 AN: 2112

Alfa AF: 0.242 Hom.: 18852

Bravo AF: 0.227

Asia WGS AF: 0.251 AC: 871 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.0
DANN	Benign	0.62
PhyloP100		-0.80

Splicing

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

Other links and lift over

dbSNP: rs10102377; hg19: chr8-83762822;