rs10487506

Variant names:

• chr7-128238102-G-A
• rs10487506
• ENST00000785131.1:n.169-16562C>T

Variant summary

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

The ENST00000785131.1(ENSG00000289434):​n.169-16562C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.374 in 152,128 control chromosomes in the GnomAD database, including 12,821 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 0.37 (12821 hom., cov: 33)
• Consequence: ENSG00000289434 ENST00000785131.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.542
• Publications: 19 publications found

Genes affected

ENSG00000289434 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.724 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
ENSG00000289434	ENST00000785131.1	n.169-16562C>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.374 AC: 56850 AN: 152008 Hom.: 12817 Cov.: 33

Gnomad AFR AF: 0.124

Gnomad AMI AF: 0.438

Gnomad AMR AF: 0.436

Gnomad ASJ AF: 0.418

Gnomad EAS AF: 0.743

Gnomad SAS AF: 0.525

Gnomad FIN AF: 0.508

Gnomad MID AF: 0.443

Gnomad NFE AF: 0.449

Gnomad OTH AF: 0.377

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

GnomAD4 genome AF: 0.374 AC: 56874 AN: 152128 Hom.: 12821 Cov.: 33 AF XY: 0.384 AC XY: 28568 AN XY: 74348

African (AFR) AF: 0.124 AC: 5144 AN: 41498

American (AMR) AF: 0.436 AC: 6656 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.418 AC: 1452 AN: 3472

East Asian (EAS) AF: 0.744 AC: 3851 AN: 5178

South Asian (SAS) AF: 0.525 AC: 2532 AN: 4820

European-Finnish (FIN) AF: 0.508 AC: 5373 AN: 10574

Middle Eastern (MID) AF: 0.435 AC: 128 AN: 294

European-Non Finnish (NFE) AF: 0.449 AC: 30535 AN: 67988

Other (OTH) AF: 0.381 AC: 804 AN: 2112

Alfa AF: 0.424 Hom.: 23853

Bravo AF: 0.354

Asia WGS AF: 0.626 AC: 2173 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.38
DANN	Benign	0.58
PhyloP100		-0.54

Splicing

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

Other links and lift over

dbSNP: rs10487506; hg19: chr7-127878155;