1-185675531-T-C

Variant names:

• chr1-185675531-T-C
• rs10489711
• ENST00000785885.1:n.858+1465T>C

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.858+1465T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0474 in 152,254 control chromosomes in the GnomAD database, including 414 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 0.047 (414 hom., cov: 32)
• Consequence: GS1-204I12.4 ENST00000785885.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.94
• Publications: 3 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=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.13 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000785885.1. 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
	GS1-204I12.4	ENST00000785885.1		n.858+1465T>C		intron	N/A
	GS1-204I12.4	ENST00000785886.1		n.169-3918T>C		intron	N/A
	GS1-204I12.4	ENST00000785887.1		n.124-3918T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0472 AC: 7182 AN: 152136 Hom.: 404 Cov.: 32

Gnomad AFR AF: 0.133

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0244

Gnomad ASJ AF: 0.0501

Gnomad EAS AF: 0.0464

Gnomad SAS AF: 0.0325

Gnomad FIN AF: 0.0102

Gnomad MID AF: 0.0411

Gnomad NFE AF: 0.00753

Gnomad OTH AF: 0.0511

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

GnomAD4 genome AF: 0.0474 AC: 7218 AN: 152254 Hom.: 414 Cov.: 32 AF XY: 0.0459 AC XY: 3420 AN XY: 74448

African (AFR) AF: 0.133 AC: 5533 AN: 41532

American (AMR) AF: 0.0243 AC: 372 AN: 15282

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

East Asian (EAS) AF: 0.0467 AC: 242 AN: 5182

South Asian (SAS) AF: 0.0325 AC: 157 AN: 4830

European-Finnish (FIN) AF: 0.0102 AC: 108 AN: 10626

Middle Eastern (MID) AF: 0.0442 AC: 13 AN: 294

European-Non Finnish (NFE) AF: 0.00753 AC: 512 AN: 68008

Other (OTH) AF: 0.0506 AC: 107 AN: 2116

Alfa AF: 0.0208 Hom.: 489

Bravo AF: 0.0543

Asia WGS AF: 0.0660 AC: 231 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.014
DANN	Benign	0.60
PhyloP100		-1.9

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: rs10489711;

hg19: chr1-185644663;