rs1325507

Variant names:

• chr1-152646788-G-A
• rs1325507
• ENST00000802896.1:n.421-2050C>T

Variant summary

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

The ENST00000802896.1(ENSG00000304363):​n.421-2050C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.172 in 152,088 control chromosomes in the GnomAD database, including 3,137 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 0.17 (3137 hom., cov: 32)
• Consequence: ENSG00000304363 ENST00000802896.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.434
• Publications: 5 publications found

Genes affected

ENSG00000304363 (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 (AFR) allele frequency at 95% confidence interval = 0.326 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000802896.1. 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
	ENSG00000304363	ENST00000802896.1		n.421-2050C>T		intron	N/A
	ENSG00000304363	ENST00000802897.1		n.235-2050C>T		intron	N/A
	ENSG00000304363	ENST00000802898.1		n.198-2050C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.172 AC: 26066 AN: 151970 Hom.: 3122 Cov.: 32

Gnomad AFR AF: 0.331

Gnomad AMI AF: 0.0121

Gnomad AMR AF: 0.144

Gnomad ASJ AF: 0.0834

Gnomad EAS AF: 0.292

Gnomad SAS AF: 0.145

Gnomad FIN AF: 0.160

Gnomad MID AF: 0.136

Gnomad NFE AF: 0.0826

Gnomad OTH AF: 0.156

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

GnomAD4 genome AF: 0.172 AC: 26110 AN: 152088 Hom.: 3137 Cov.: 32 AF XY: 0.174 AC XY: 12967 AN XY: 74362

African (AFR) AF: 0.331 AC: 13714 AN: 41422

American (AMR) AF: 0.144 AC: 2201 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.0834 AC: 289 AN: 3466

East Asian (EAS) AF: 0.292 AC: 1504 AN: 5158

South Asian (SAS) AF: 0.144 AC: 693 AN: 4814

European-Finnish (FIN) AF: 0.160 AC: 1699 AN: 10602

Middle Eastern (MID) AF: 0.133 AC: 39 AN: 294

European-Non Finnish (NFE) AF: 0.0826 AC: 5619 AN: 68010

Other (OTH) AF: 0.161 AC: 341 AN: 2112

Alfa AF: 0.112 Hom.: 867

Bravo AF: 0.177

Asia WGS AF: 0.244 AC: 848 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	5.1
DANN	Benign	0.66
PhyloP100		0.43

Splicing

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

Other links and lift over

dbSNP: rs1325507; hg19: chr1-152619264;