XR_001738340.2:n.1067-5388C>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 XR_001738340.2(LOC107985239):​n.1067-5388C>T variant causes a intron 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: LOC107985239 XR_001738340.2 intron
• 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

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.853C>T		non_coding_transcript_exon	Exon 4 of 7
	GS1-204I12.4	ENST00000785886.1		n.169-5388C>T		intron	N/A
	GS1-204I12.4	ENST00000785887.1		n.124-5388C>T		intron	N/A

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 v4.9

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;