rs7915120

Variant names:

• chr10-114025486-A-G
• rs7915120
• ENST00000729868.1:n.343-2851T>C

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000729868.1(ENSG00000295421):​n.343-2851T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.271 in 152,054 control chromosomes in the GnomAD database, including 5,790 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 0.27 (5790 hom., cov: 32)
• Consequence: ENSG00000295421 ENST00000729868.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.576
• Publications: 3 publications found

Genes affected

ENSG00000295421 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.41).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.32 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
ENSG00000295421	ENST00000729868.1	n.343-2851T>C		intron_variant	Intron 2 of 2
ENSG00000295421	ENST00000729869.1	n.125-2851T>C		intron_variant	Intron 1 of 1
ENSG00000295421	ENST00000729870.1	n.234-2851T>C		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.271 AC: 41165 AN: 151936 Hom.: 5760 Cov.: 32

Gnomad AFR AF: 0.324

Gnomad AMI AF: 0.181

Gnomad AMR AF: 0.310

Gnomad ASJ AF: 0.157

Gnomad EAS AF: 0.160

Gnomad SAS AF: 0.191

Gnomad FIN AF: 0.263

Gnomad MID AF: 0.158

Gnomad NFE AF: 0.254

Gnomad OTH AF: 0.249

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

GnomAD4 genome AF: 0.271 AC: 41255 AN: 152054 Hom.: 5790 Cov.: 32 AF XY: 0.270 AC XY: 20077 AN XY: 74348

African (AFR) AF: 0.325 AC: 13452 AN: 41432

American (AMR) AF: 0.310 AC: 4740 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.157 AC: 545 AN: 3472

East Asian (EAS) AF: 0.160 AC: 830 AN: 5176

South Asian (SAS) AF: 0.191 AC: 922 AN: 4816

European-Finnish (FIN) AF: 0.263 AC: 2784 AN: 10566

Middle Eastern (MID) AF: 0.160 AC: 47 AN: 294

European-Non Finnish (NFE) AF: 0.254 AC: 17241 AN: 68006

Other (OTH) AF: 0.250 AC: 529 AN: 2112

Alfa AF: 0.258 Hom.: 4176

Bravo AF: 0.279

Asia WGS AF: 0.226 AC: 785 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.41
CADD	Benign	18
DANN	Benign	0.77
PhyloP100		0.58

Splicing

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

Other links and lift over

dbSNP: rs7915120; hg19: chr10-115785245;