rs10489712

Variant names:

• chr1-185678060-A-G
• rs10489712
• ENST00000785885.1:n.859-139A>G

Variant summary

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

The ENST00000785885.1(GS1-204I12.4):​n.859-139A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0662 in 152,210 control chromosomes in the GnomAD database, including 882 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 0.066 (882 hom., cov: 32)
• Consequence: GS1-204I12.4 ENST00000785885.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0230
• Publications: 0 publications found

Genes affected

GS1-204I12.4 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.194 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC107985239	XR_001738340.2	n.1067-1389A>G		intron_variant	Intron 1 of 2
LOC107985239	XR_001738339.2	n.-137A>G		upstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GS1-204I12.4	ENST00000785885.1	n.859-139A>G		intron_variant	Intron 4 of 6
GS1-204I12.4	ENST00000785886.1	n.169-1389A>G		intron_variant	Intron 2 of 3
GS1-204I12.4	ENST00000785887.1	n.124-1389A>G		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.0659 AC: 10028 AN: 152092 Hom.: 870 Cov.: 32

Gnomad AFR AF: 0.197

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0322

Gnomad ASJ AF: 0.0501

Gnomad EAS AF: 0.0466

Gnomad SAS AF: 0.0329

Gnomad FIN AF: 0.0102

Gnomad MID AF: 0.0538

Gnomad NFE AF: 0.00797

Gnomad OTH AF: 0.0640

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

GnomAD4 genome AF: 0.0662 AC: 10071 AN: 152210 Hom.: 882 Cov.: 32 AF XY: 0.0638 AC XY: 4746 AN XY: 74416

African (AFR) AF: 0.198 AC: 8204 AN: 41510

American (AMR) AF: 0.0322 AC: 492 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.0501 AC: 174 AN: 3472

East Asian (EAS) AF: 0.0469 AC: 243 AN: 5184

South Asian (SAS) AF: 0.0329 AC: 159 AN: 4826

European-Finnish (FIN) AF: 0.0102 AC: 108 AN: 10612

Middle Eastern (MID) AF: 0.0578 AC: 17 AN: 294

European-Non Finnish (NFE) AF: 0.00794 AC: 540 AN: 67994

Other (OTH) AF: 0.0633 AC: 134 AN: 2116

Alfa AF: 0.0385 Hom.: 175

Bravo AF: 0.0762

Asia WGS AF: 0.0710 AC: 246 AN: 3460

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	6.1
DANN	Benign	0.86
PhyloP100		-0.023

Splicing

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

Other links and lift over

dbSNP: rs10489712; hg19: chr1-185647192;