rs10787516

Variant names:

• chr10-114054165-C-T
• rs10787516
• ENST00000804402.1:n.194-6970G>A

Variant summary

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

The ENST00000804402.1(ENSG00000304538):​n.194-6970G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.415 in 152,064 control chromosomes in the GnomAD database, including 14,925 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 0.41 (14925 hom., cov: 33)
• Consequence: ENSG00000304538 ENST00000804402.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.143
• Publications: 9 publications found

Genes affected

ENSG00000304538 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.597 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124902554	XR_007062383.1	n.194-6970G>A		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000304538	ENST00000804402.1	n.194-6970G>A		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.415 AC: 63061 AN: 151946 Hom.: 14929 Cov.: 33

Gnomad AFR AF: 0.172

Gnomad AMI AF: 0.495

Gnomad AMR AF: 0.460

Gnomad ASJ AF: 0.465

Gnomad EAS AF: 0.616

Gnomad SAS AF: 0.561

Gnomad FIN AF: 0.550

Gnomad MID AF: 0.475

Gnomad NFE AF: 0.502

Gnomad OTH AF: 0.418

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

GnomAD4 genome AF: 0.415 AC: 63064 AN: 152064 Hom.: 14925 Cov.: 33 AF XY: 0.423 AC XY: 31426 AN XY: 74312

African (AFR) AF: 0.172 AC: 7118 AN: 41476

American (AMR) AF: 0.460 AC: 7037 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.465 AC: 1611 AN: 3468

East Asian (EAS) AF: 0.615 AC: 3181 AN: 5172

South Asian (SAS) AF: 0.561 AC: 2704 AN: 4818

European-Finnish (FIN) AF: 0.550 AC: 5801 AN: 10540

Middle Eastern (MID) AF: 0.469 AC: 138 AN: 294

European-Non Finnish (NFE) AF: 0.502 AC: 34143 AN: 67984

Other (OTH) AF: 0.417 AC: 881 AN: 2114

Alfa AF: 0.463 Hom.: 46219

Bravo AF: 0.392

Asia WGS AF: 0.522 AC: 1816 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	3.4
DANN	Benign	0.48
PhyloP100		-0.14

Splicing

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

Other links and lift over

dbSNP: rs10787516; hg19: chr10-115813924;