rs1786330

Variant names:

• chr8-100679902-C-T
• rs1786330
• ENST00000849485.1:n.164+2921C>T

Variant summary

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

The ENST00000849485.1(ENSG00000310385):​n.164+2921C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.284 in 151,934 control chromosomes in the GnomAD database, including 6,238 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 0.28 (6238 hom., cov: 31)
• Consequence: ENSG00000310385 ENST00000849485.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0410
• Publications: 7 publications found

Genes affected

ENSG00000310385 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.341 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
ENSG00000310385	ENST00000849485.1	n.164+2921C>T		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.284 AC: 43094 AN: 151814 Hom.: 6237 Cov.: 31

Gnomad AFR AF: 0.230

Gnomad AMI AF: 0.377

Gnomad AMR AF: 0.233

Gnomad ASJ AF: 0.289

Gnomad EAS AF: 0.241

Gnomad SAS AF: 0.356

Gnomad FIN AF: 0.357

Gnomad MID AF: 0.274

Gnomad NFE AF: 0.313

Gnomad OTH AF: 0.277

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

GnomAD4 genome AF: 0.284 AC: 43096 AN: 151934 Hom.: 6238 Cov.: 31 AF XY: 0.285 AC XY: 21159 AN XY: 74238

African (AFR) AF: 0.230 AC: 9510 AN: 41400

American (AMR) AF: 0.233 AC: 3558 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.289 AC: 1002 AN: 3470

East Asian (EAS) AF: 0.240 AC: 1243 AN: 5170

South Asian (SAS) AF: 0.355 AC: 1712 AN: 4816

European-Finnish (FIN) AF: 0.357 AC: 3769 AN: 10554

Middle Eastern (MID) AF: 0.257 AC: 75 AN: 292

European-Non Finnish (NFE) AF: 0.313 AC: 21298 AN: 67950

Other (OTH) AF: 0.278 AC: 585 AN: 2108

Alfa AF: 0.310 Hom.: 1374

Bravo AF: 0.269

Asia WGS AF: 0.280 AC: 974 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	4.1
DANN	Benign	0.50
PhyloP100		0.041

Splicing

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

Other links and lift over

dbSNP: rs1786330; hg19: chr8-101692130; COSMIC: COSV72762458;