10-120327002-C-T

Variant names:

• chr10-120327002-C-T
• rs7092549
• ENST00000794040.1:n.277-9519C>T

Variant summary

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

The ENST00000794040.1(ENSG00000303377):​n.277-9519C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.221 in 152,018 control chromosomes in the GnomAD database, including 4,062 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 0.22 (4062 hom., cov: 32)
• Consequence: ENSG00000303377 ENST00000794040.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.590
• Publications: 2 publications found

Genes affected

ENSG00000303377 (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 (EAS) allele frequency at 95% confidence interval = 0.24 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000794040.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000303377	ENST00000794040.1		n.277-9519C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.221 AC: 33606 AN: 151900 Hom.: 4059 Cov.: 32

Gnomad AFR AF: 0.179

Gnomad AMI AF: 0.364

Gnomad AMR AF: 0.164

Gnomad ASJ AF: 0.253

Gnomad EAS AF: 0.252

Gnomad SAS AF: 0.192

Gnomad FIN AF: 0.403

Gnomad MID AF: 0.0892

Gnomad NFE AF: 0.228

Gnomad OTH AF: 0.219

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

GnomAD4 genome AF: 0.221 AC: 33610 AN: 152018 Hom.: 4062 Cov.: 32 AF XY: 0.227 AC XY: 16893 AN XY: 74314

African (AFR) AF: 0.179 AC: 7441 AN: 41490

American (AMR) AF: 0.164 AC: 2499 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.253 AC: 878 AN: 3470

East Asian (EAS) AF: 0.251 AC: 1297 AN: 5162

South Asian (SAS) AF: 0.192 AC: 922 AN: 4810

European-Finnish (FIN) AF: 0.403 AC: 4248 AN: 10538

Middle Eastern (MID) AF: 0.0822 AC: 24 AN: 292

European-Non Finnish (NFE) AF: 0.228 AC: 15510 AN: 67974

Other (OTH) AF: 0.218 AC: 459 AN: 2110

Alfa AF: 0.154 Hom.: 413

Bravo AF: 0.203

Asia WGS AF: 0.225 AC: 783 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.95
DANN	Benign	0.41
PhyloP100		-0.59

Splicing

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

Other links and lift over

dbSNP: rs7092549; hg19: chr10-122086514;