1-147754660-G-A

Variant names:

• chr1-147754660-G-A
• rs1891498
• ENST00000721952.1:n.387-17037C>T

Variant summary

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

The ENST00000721952.1(ENSG00000294222):​n.387-17037C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.164 in 152,224 control chromosomes in the GnomAD database, including 2,327 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 0.16 (2327 hom., cov: 33)
• Consequence: ENSG00000294222 ENST00000721952.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.07
• Publications: 6 publications found

Genes affected

ENSG00000294222 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.216 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000721952.1. 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
	ENSG00000294222	ENST00000721952.1		n.387-17037C>T		intron	N/A
	ENSG00000294222	ENST00000721953.1		n.389-17037C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.164 AC: 24926 AN: 152106 Hom.: 2326 Cov.: 33

Gnomad AFR AF: 0.0920

Gnomad AMI AF: 0.300

Gnomad AMR AF: 0.149

Gnomad ASJ AF: 0.130

Gnomad EAS AF: 0.0792

Gnomad SAS AF: 0.0507

Gnomad FIN AF: 0.211

Gnomad MID AF: 0.0665

Gnomad NFE AF: 0.219

Gnomad OTH AF: 0.165

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

GnomAD4 genome AF: 0.164 AC: 24934 AN: 152224 Hom.: 2327 Cov.: 33 AF XY: 0.159 AC XY: 11863 AN XY: 74412

African (AFR) AF: 0.0920 AC: 3821 AN: 41554

American (AMR) AF: 0.148 AC: 2268 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.130 AC: 453 AN: 3472

East Asian (EAS) AF: 0.0788 AC: 409 AN: 5188

South Asian (SAS) AF: 0.0516 AC: 249 AN: 4828

European-Finnish (FIN) AF: 0.211 AC: 2233 AN: 10590

Middle Eastern (MID) AF: 0.0714 AC: 21 AN: 294

European-Non Finnish (NFE) AF: 0.219 AC: 14862 AN: 67986

Other (OTH) AF: 0.164 AC: 346 AN: 2108

Alfa AF: 0.191 Hom.: 6095

Bravo AF: 0.158

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.13
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs1891498; hg19: chr1-147226791;