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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000804402.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000304538	ENST00000804402.1		n.194-6970G>A		intron	N/A

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 v4.9

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs10787516;

hg19: chr10-115813924;