1-98376273-T-C

Variant names:

• chr1-98376273-T-C
• rs7525553

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.849 in 152,174 control chromosomes in the GnomAD database, including 55,539 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 0.85 (55539 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.433

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.919 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.849 AC: 129147 AN: 152056 Hom.: 55506 Cov.: 33

Gnomad AFR AF: 0.927

Gnomad AMI AF: 0.838

Gnomad AMR AF: 0.718

Gnomad ASJ AF: 0.814

Gnomad EAS AF: 0.549

Gnomad SAS AF: 0.833

Gnomad FIN AF: 0.854

Gnomad MID AF: 0.870

Gnomad NFE AF: 0.857

Gnomad OTH AF: 0.835

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

GnomAD4 genome AF: 0.849 AC: 129229 AN: 152174 Hom.: 55539 Cov.: 33 AF XY: 0.847 AC XY: 62976 AN XY: 74386

Gnomad4 AFR AF: 0.927

Gnomad4 AMR AF: 0.717

Gnomad4 ASJ AF: 0.814

Gnomad4 EAS AF: 0.549

Gnomad4 SAS AF: 0.834

Gnomad4 FIN AF: 0.854

Gnomad4 NFE AF: 0.857

Gnomad4 OTH AF: 0.829

Alfa AF: 0.846 Hom.: 31097

Bravo AF: 0.838

Asia WGS AF: 0.696 AC: 2424 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	3.7
DANN	Benign	0.68

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7525553; hg19: chr1-98841829;