rs10513767

Variant names:

• chr3-180097403-G-A
• rs10513767
• ENST00000785992.1:n.210-10887G>A

Variant summary

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

The ENST00000785992.1(ENSG00000287645):​n.210-10887G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0863 in 152,156 control chromosomes in the GnomAD database, including 912 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 0.086 (912 hom., cov: 33)
• Consequence: ENSG00000287645 ENST00000785992.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.673
• Publications: 6 publications found

Genes affected

ENSG00000287645 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.183 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
ENSG00000287645	ENST00000785992.1	n.210-10887G>A		intron_variant	Intron 2 of 4

Frequencies

GnomAD3 genomes AF: 0.0861 AC: 13097 AN: 152038 Hom.: 908 Cov.: 33

Gnomad AFR AF: 0.187

Gnomad AMI AF: 0.0582

Gnomad AMR AF: 0.0609

Gnomad ASJ AF: 0.0718

Gnomad EAS AF: 0.00788

Gnomad SAS AF: 0.131

Gnomad FIN AF: 0.0321

Gnomad MID AF: 0.0510

Gnomad NFE AF: 0.0435

Gnomad OTH AF: 0.0742

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

GnomAD4 genome AF: 0.0863 AC: 13129 AN: 152156 Hom.: 912 Cov.: 33 AF XY: 0.0854 AC XY: 6356 AN XY: 74410

African (AFR) AF: 0.187 AC: 7749 AN: 41480

American (AMR) AF: 0.0610 AC: 932 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.0718 AC: 249 AN: 3468

East Asian (EAS) AF: 0.00770 AC: 40 AN: 5192

South Asian (SAS) AF: 0.131 AC: 631 AN: 4816

European-Finnish (FIN) AF: 0.0321 AC: 340 AN: 10606

Middle Eastern (MID) AF: 0.0582 AC: 17 AN: 292

European-Non Finnish (NFE) AF: 0.0434 AC: 2954 AN: 67992

Other (OTH) AF: 0.0777 AC: 164 AN: 2112

Alfa AF: 0.0594 Hom.: 528

Bravo AF: 0.0896

Asia WGS AF: 0.0970 AC: 339 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.30
DANN	Benign	0.41
PhyloP100		-0.67

Splicing

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

Other links and lift over

dbSNP: rs10513767; hg19: chr3-179815191;