10-3797822-G-T

Variant names:

• chr10-3797822-G-T
• rs10508266
• ENST00000686778.1:n.333+5183G>T

Variant summary

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

The ENST00000686778.1(ENSG00000288755):​n.333+5183G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.194 in 152,002 control chromosomes in the GnomAD database, including 3,616 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 (3616 hom., cov: 32)
• Consequence: ENSG00000288755 ENST00000686778.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.269
• Publications: 4 publications found

Genes affected

ENSG00000288755 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.292 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
ENSG00000288755	ENST00000686778.1	n.333+5183G>T		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.194 AC: 29482 AN: 151884 Hom.: 3621 Cov.: 32

Gnomad AFR AF: 0.0473

Gnomad AMI AF: 0.192

Gnomad AMR AF: 0.219

Gnomad ASJ AF: 0.343

Gnomad EAS AF: 0.299

Gnomad SAS AF: 0.304

Gnomad FIN AF: 0.261

Gnomad MID AF: 0.293

Gnomad NFE AF: 0.243

Gnomad OTH AF: 0.216

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

GnomAD4 genome AF: 0.194 AC: 29475 AN: 152002 Hom.: 3616 Cov.: 32 AF XY: 0.198 AC XY: 14673 AN XY: 74252

African (AFR) AF: 0.0472 AC: 1960 AN: 41486

American (AMR) AF: 0.218 AC: 3336 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.343 AC: 1192 AN: 3472

East Asian (EAS) AF: 0.299 AC: 1546 AN: 5174

South Asian (SAS) AF: 0.305 AC: 1467 AN: 4804

European-Finnish (FIN) AF: 0.261 AC: 2746 AN: 10532

Middle Eastern (MID) AF: 0.277 AC: 81 AN: 292

European-Non Finnish (NFE) AF: 0.243 AC: 16520 AN: 67952

Other (OTH) AF: 0.214 AC: 452 AN: 2110

Alfa AF: 0.226 Hom.: 10977

Bravo AF: 0.185

Asia WGS AF: 0.226 AC: 789 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.17
DANN	Benign	0.33
PhyloP100		-0.27

Splicing

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

Other links and lift over

dbSNP: rs10508266; hg19: chr10-3840014;