rs1332498

Variant names:

• chr1-152717972-T-C
• rs1332498
• ENST00000802896.1:n.80+27507A>G

Variant summary

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

The ENST00000802896.1(ENSG00000304363):​n.80+27507A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.381 in 151,770 control chromosomes in the GnomAD database, including 11,581 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 0.38 (11581 hom., cov: 31)
• Consequence: ENSG00000304363 ENST00000802896.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.800
• Publications: 9 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=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.494 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

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
	ENSG00000304363	ENST00000802896.1		n.80+27507A>G		intron	N/A
	ENSG00000304363	ENST00000802897.1		n.68+27507A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.381 AC: 57738 AN: 151650 Hom.: 11562 Cov.: 31

Gnomad AFR AF: 0.499

Gnomad AMI AF: 0.286

Gnomad AMR AF: 0.374

Gnomad ASJ AF: 0.270

Gnomad EAS AF: 0.163

Gnomad SAS AF: 0.225

Gnomad FIN AF: 0.305

Gnomad MID AF: 0.347

Gnomad NFE AF: 0.357

Gnomad OTH AF: 0.372

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

GnomAD4 genome AF: 0.381 AC: 57794 AN: 151770 Hom.: 11581 Cov.: 31 AF XY: 0.375 AC XY: 27797 AN XY: 74178

African (AFR) AF: 0.499 AC: 20634 AN: 41324

American (AMR) AF: 0.374 AC: 5706 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.270 AC: 935 AN: 3468

East Asian (EAS) AF: 0.164 AC: 841 AN: 5140

South Asian (SAS) AF: 0.225 AC: 1085 AN: 4818

European-Finnish (FIN) AF: 0.305 AC: 3207 AN: 10518

Middle Eastern (MID) AF: 0.332 AC: 97 AN: 292

European-Non Finnish (NFE) AF: 0.357 AC: 24252 AN: 67916

Other (OTH) AF: 0.368 AC: 776 AN: 2106

Alfa AF: 0.358 Hom.: 14778

Bravo AF: 0.389

Asia WGS AF: 0.211 AC: 735 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	1.1
DANN	Benign	0.69
PhyloP100		-0.80

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: rs1332498;

hg19: chr1-152690448;