1-22149323-G-A

Variant names:

• chr1-22149323-G-A
• rs10493011
• ENST00000648968.1:n.56-5580G>A

Variant summary

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

The ENST00000648968.1(ENSG00000285873):​n.56-5580G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0479 in 152,168 control chromosomes in the GnomAD database, including 292 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 0.048 (292 hom., cov: 32)
• Consequence: ENSG00000285873 ENST00000648968.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0150
• Publications: 1 publications found

Genes affected

ENSG00000285873 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.11 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000648968.1. 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
	ENSG00000285873	ENST00000648968.1		n.56-5580G>A		intron	N/A
	ENSG00000285873	ENST00000808862.1		n.36+6419G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0479 AC: 7289 AN: 152050 Hom.: 294 Cov.: 32

Gnomad AFR AF: 0.0830

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0891

Gnomad ASJ AF: 0.0452

Gnomad EAS AF: 0.118

Gnomad SAS AF: 0.0342

Gnomad FIN AF: 0.0609

Gnomad MID AF: 0.0222

Gnomad NFE AF: 0.0119

Gnomad OTH AF: 0.0464

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

GnomAD4 genome AF: 0.0479 AC: 7291 AN: 152168 Hom.: 292 Cov.: 32 AF XY: 0.0502 AC XY: 3733 AN XY: 74392

African (AFR) AF: 0.0828 AC: 3438 AN: 41502

American (AMR) AF: 0.0892 AC: 1365 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.0452 AC: 157 AN: 3472

East Asian (EAS) AF: 0.118 AC: 609 AN: 5170

South Asian (SAS) AF: 0.0342 AC: 165 AN: 4820

European-Finnish (FIN) AF: 0.0609 AC: 645 AN: 10586

Middle Eastern (MID) AF: 0.0170 AC: 5 AN: 294

European-Non Finnish (NFE) AF: 0.0119 AC: 809 AN: 68000

Other (OTH) AF: 0.0464 AC: 98 AN: 2114

Alfa AF: 0.0293 Hom.: 31

Bravo AF: 0.0508

Asia WGS AF: 0.0700 AC: 246 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	2.3
DANN	Benign	0.41
PhyloP100		-0.015

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs10493011;

hg19: chr1-22475816;