1-185674061-C-T

Variant names:

• chr1-185674061-C-T
• rs10489708
• ENST00000785885.1:n.853C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The ENST00000785885.1(GS1-204I12.4):​n.853C>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0216 in 152,282 control chromosomes in the GnomAD database, including 65 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 0.022 (65 hom., cov: 32)
• Consequence: GS1-204I12.4 ENST00000785885.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0190
• 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=-0.59).
• BS1: Variant frequency is greater than expected in population afr. GnomAd4 allele frequency = 0.0216 (3284/152282) while in subpopulation AFR AF = 0.0472 (1960/41562). AF 95% confidence interval is 0.0454. There are 65 homozygotes in GnomAd4. There are 1595 alleles in the male GnomAd4 subpopulation. Median coverage is 32. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 65 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC107985239	XR_001738340.2	n.1067-5388C>T		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GS1-204I12.4	ENST00000785885.1	n.853C>T		non_coding_transcript_exon_variant	Exon 4 of 7
GS1-204I12.4	ENST00000785886.1	n.169-5388C>T		intron_variant	Intron 2 of 3
GS1-204I12.4	ENST00000785887.1	n.124-5388C>T		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.0215 AC: 3278 AN: 152164 Hom.: 64 Cov.: 32

Gnomad AFR AF: 0.0471

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0157

Gnomad ASJ AF: 0.0501

Gnomad EAS AF: 0.0352

Gnomad SAS AF: 0.0317

Gnomad FIN AF: 0.00207

Gnomad MID AF: 0.0380

Gnomad NFE AF: 0.00695

Gnomad OTH AF: 0.0330

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

GnomAD4 genome AF: 0.0216 AC: 3284 AN: 152282 Hom.: 65 Cov.: 32 AF XY: 0.0214 AC XY: 1595 AN XY: 74452

African (AFR) AF: 0.0472 AC: 1960 AN: 41562

American (AMR) AF: 0.0156 AC: 239 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.0501 AC: 174 AN: 3470

East Asian (EAS) AF: 0.0351 AC: 182 AN: 5182

South Asian (SAS) AF: 0.0317 AC: 153 AN: 4824

European-Finnish (FIN) AF: 0.00207 AC: 22 AN: 10610

Middle Eastern (MID) AF: 0.0408 AC: 12 AN: 294

European-Non Finnish (NFE) AF: 0.00695 AC: 473 AN: 68024

Other (OTH) AF: 0.0326 AC: 69 AN: 2116

Alfa AF: 0.00962 Hom.: 5

Bravo AF: 0.0250

Asia WGS AF: 0.0460 AC: 159 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.59
CADD	Benign	2.0
DANN	Benign	0.81
PhyloP100		-0.019

Splicing

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

Other links and lift over

dbSNP: rs10489708; hg19: chr1-185643193;