10-30810210-C-T

Variant names:

• chr10-30810210-C-T
• rs1340949
• ENST00000790382.1:n.238G>A

Variant summary

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

The ENST00000790382.1(ENSG00000302909):​n.238G>A variant causes a splice region, non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.652 in 152,028 control chromosomes in the GnomAD database, including 33,258 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 0.65 (33258 hom., cov: 32)
• Consequence: ENSG00000302909 ENST00000790382.1 splice_region, non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.145
• Publications: 5 publications found

Genes affected

ENSG00000302909 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.813 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000790382.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000302909	ENST00000790382.1		n.238G>A		splice_region non_coding_transcript_exon	Exon 2 of 3
	ENSG00000302909	ENST00000790383.1		n.303G>A		splice_region non_coding_transcript_exon	Exon 2 of 3
	ENSG00000302909	ENST00000790380.1		n.68-1804G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.652 AC: 99069 AN: 151910 Hom.: 33206 Cov.: 32

Gnomad AFR AF: 0.820

Gnomad AMI AF: 0.370

Gnomad AMR AF: 0.654

Gnomad ASJ AF: 0.585

Gnomad EAS AF: 0.674

Gnomad SAS AF: 0.601

Gnomad FIN AF: 0.616

Gnomad MID AF: 0.491

Gnomad NFE AF: 0.567

Gnomad OTH AF: 0.608

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

GnomAD4 genome AF: 0.652 AC: 99181 AN: 152028 Hom.: 33258 Cov.: 32 AF XY: 0.653 AC XY: 48552 AN XY: 74298

African (AFR) AF: 0.820 AC: 34021 AN: 41488

American (AMR) AF: 0.654 AC: 9998 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.585 AC: 2032 AN: 3472

East Asian (EAS) AF: 0.674 AC: 3474 AN: 5152

South Asian (SAS) AF: 0.600 AC: 2889 AN: 4814

European-Finnish (FIN) AF: 0.616 AC: 6519 AN: 10576

Middle Eastern (MID) AF: 0.500 AC: 147 AN: 294

European-Non Finnish (NFE) AF: 0.567 AC: 38490 AN: 67940

Other (OTH) AF: 0.608 AC: 1274 AN: 2096

Alfa AF: 0.585 Hom.: 41378

Bravo AF: 0.662

Asia WGS AF: 0.631 AC: 2196 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.21
DANN	Benign	0.47
PhyloP100		-0.14

Splicing

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

Other links and lift over

dbSNP: rs1340949; hg19: chr10-31099139;