1-157938654-A-G

Variant names:

• chr1-157938654-A-G
• rs10494321
• ENST00000422062.1:n.262-4010A>G

Variant summary

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

The ENST00000422062.1(ENSG00000291226):​n.262-4010A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.313 in 152,096 control chromosomes in the GnomAD database, including 7,926 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 0.31 (7926 hom., cov: 32)
• Consequence: ENSG00000291226 ENST00000422062.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0990
• Publications: 4 publications found

Genes affected

ENSG00000291226 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.342 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000422062.1. 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
	LOC105371458	NR_135760.1		n.340-7002A>G		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000291226	ENST00000422062.1	TSL:2	n.262-4010A>G		intron	N/A
	ENSG00000291226	ENST00000452528.5	TSL:2	n.333-7002A>G		intron	N/A
	ENSG00000291226	ENST00000789662.1		n.342-7002A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.313 AC: 47498 AN: 151978 Hom.: 7912 Cov.: 32

Gnomad AFR AF: 0.347

Gnomad AMI AF: 0.310

Gnomad AMR AF: 0.215

Gnomad ASJ AF: 0.161

Gnomad EAS AF: 0.0786

Gnomad SAS AF: 0.238

Gnomad FIN AF: 0.404

Gnomad MID AF: 0.139

Gnomad NFE AF: 0.332

Gnomad OTH AF: 0.273

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

GnomAD4 genome AF: 0.313 AC: 47554 AN: 152096 Hom.: 7926 Cov.: 32 AF XY: 0.310 AC XY: 23021 AN XY: 74352

African (AFR) AF: 0.347 AC: 14403 AN: 41504

American (AMR) AF: 0.215 AC: 3281 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.161 AC: 558 AN: 3462

East Asian (EAS) AF: 0.0787 AC: 408 AN: 5182

South Asian (SAS) AF: 0.240 AC: 1155 AN: 4822

European-Finnish (FIN) AF: 0.404 AC: 4272 AN: 10570

Middle Eastern (MID) AF: 0.143 AC: 42 AN: 294

European-Non Finnish (NFE) AF: 0.332 AC: 22581 AN: 67964

Other (OTH) AF: 0.272 AC: 572 AN: 2106

Alfa AF: 0.312 Hom.: 24616

Bravo AF: 0.297

Asia WGS AF: 0.186 AC: 645 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.5
DANN	Benign	0.53
PhyloP100		-0.099

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: rs10494321;

hg19: chr1-157908444;