rs4072643

Variant names:

• chr1-178565086-C-T
• rs4072643
• XR_007066747.1:n.2972G>A

Variant summary

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

The XR_007066747.1(LOC105371632):​n.2972G>A 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 0.0746 in 152,242 control chromosomes in the GnomAD database, including 1,288 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 0.075 (1288 hom., cov: 32)
• Consequence: LOC105371632 XR_007066747.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.392
• Publications: 2 publications found

Genes affected

LOC105371632 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.234 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000750010.1. 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
	ENSG00000297676	ENST00000750010.1		n.379-5078G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0744 AC: 11322 AN: 152124 Hom.: 1280 Cov.: 32

Gnomad AFR AF: 0.238

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0401

Gnomad ASJ AF: 0.0173

Gnomad EAS AF: 0.000384

Gnomad SAS AF: 0.0188

Gnomad FIN AF: 0.00452

Gnomad MID AF: 0.0728

Gnomad NFE AF: 0.00729

Gnomad OTH AF: 0.0675

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

GnomAD4 genome AF: 0.0746 AC: 11361 AN: 152242 Hom.: 1288 Cov.: 32 AF XY: 0.0723 AC XY: 5380 AN XY: 74438

African (AFR) AF: 0.238 AC: 9889 AN: 41486

American (AMR) AF: 0.0400 AC: 613 AN: 15306

Ashkenazi Jewish (ASJ) AF: 0.0173 AC: 60 AN: 3470

East Asian (EAS) AF: 0.000385 AC: 2 AN: 5190

South Asian (SAS) AF: 0.0184 AC: 89 AN: 4824

European-Finnish (FIN) AF: 0.00452 AC: 48 AN: 10618

Middle Eastern (MID) AF: 0.0782 AC: 23 AN: 294

European-Non Finnish (NFE) AF: 0.00729 AC: 496 AN: 68032

Other (OTH) AF: 0.0668 AC: 141 AN: 2112

Alfa AF: 0.0289 Hom.: 513

Bravo AF: 0.0867

Asia WGS AF: 0.0230 AC: 80 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	5.9
DANN	Benign	0.64
PhyloP100		0.39

Splicing

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

Other links and lift over

dbSNP: rs4072643; hg19: chr1-178534221;