chr1-109907555-T-C

Variant names:

• chr1-109907555-T-C
• rs1999713
• ENST00000746665.1:n.*162T>C

Variant summary

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

The ENST00000746665.1(ENSG00000261055):​n.*162T>C variant causes a downstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.377 in 151,962 control chromosomes in the GnomAD database, including 11,497 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 0.38 (11497 hom., cov: 32)
• Consequence: ENSG00000261055 ENST00000746665.1 downstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.322
• Publications: 10 publications found

Genes affected

ENSG00000261055 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.54).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.668 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000746665.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000261055	ENST00000746665.1		n.*162T>C		downstream_gene	N/A

Frequencies

GnomAD3 genomes AF: 0.376 AC: 57156 AN: 151844 Hom.: 11476 Cov.: 32

Gnomad AFR AF: 0.314

Gnomad AMI AF: 0.372

Gnomad AMR AF: 0.480

Gnomad ASJ AF: 0.376

Gnomad EAS AF: 0.687

Gnomad SAS AF: 0.546

Gnomad FIN AF: 0.375

Gnomad MID AF: 0.367

Gnomad NFE AF: 0.355

Gnomad OTH AF: 0.411

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

GnomAD4 genome AF: 0.377 AC: 57220 AN: 151962 Hom.: 11497 Cov.: 32 AF XY: 0.383 AC XY: 28452 AN XY: 74264

African (AFR) AF: 0.314 AC: 13003 AN: 41438

American (AMR) AF: 0.480 AC: 7337 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.376 AC: 1303 AN: 3462

East Asian (EAS) AF: 0.687 AC: 3552 AN: 5170

South Asian (SAS) AF: 0.545 AC: 2621 AN: 4812

European-Finnish (FIN) AF: 0.375 AC: 3962 AN: 10552

Middle Eastern (MID) AF: 0.367 AC: 108 AN: 294

European-Non Finnish (NFE) AF: 0.355 AC: 24113 AN: 67936

Other (OTH) AF: 0.418 AC: 883 AN: 2114

Alfa AF: 0.369 Hom.: 45341

Bravo AF: 0.386

Asia WGS AF: 0.579 AC: 2009 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.54
CADD	Benign	16
DANN	Benign	0.69
PhyloP100		0.32

Splicing

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

Other links and lift over

dbSNP: rs1999713; hg19: chr1-110450177;