1-66503401-C-T

Variant names:

• chr1-66503401-C-T
• rs7533097

Variant summary

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

The variant allele was found at a frequency of 0.915 in 152,176 control chromosomes in the GnomAD database, including 63,761 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 0.92 (63761 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.160
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.976 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: 0.915 AC: 139136 AN: 152058 Hom.: 63702 Cov.: 31

Gnomad AFR AF: 0.938

Gnomad AMI AF: 0.925

Gnomad AMR AF: 0.911

Gnomad ASJ AF: 0.862

Gnomad EAS AF: 0.999

Gnomad SAS AF: 0.969

Gnomad FIN AF: 0.913

Gnomad MID AF: 0.902

Gnomad NFE AF: 0.895

Gnomad OTH AF: 0.902

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

GnomAD4 genome AF: 0.915 AC: 139254 AN: 152176 Hom.: 63761 Cov.: 31 AF XY: 0.916 AC XY: 68164 AN XY: 74386

African (AFR) AF: 0.938 AC: 38977 AN: 41542

American (AMR) AF: 0.911 AC: 13932 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.862 AC: 2992 AN: 3472

East Asian (EAS) AF: 0.999 AC: 5174 AN: 5180

South Asian (SAS) AF: 0.969 AC: 4672 AN: 4822

European-Finnish (FIN) AF: 0.913 AC: 9665 AN: 10588

Middle Eastern (MID) AF: 0.905 AC: 266 AN: 294

European-Non Finnish (NFE) AF: 0.895 AC: 60823 AN: 67966

Other (OTH) AF: 0.904 AC: 1909 AN: 2112

Alfa AF: 0.905 Hom.: 34139

Bravo AF: 0.914

Asia WGS AF: 0.976 AC: 3387 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	2.9
DANN	Benign	0.80
PhyloP100		0.16

Splicing

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

Other links and lift over

dbSNP: rs7533097; hg19: chr1-66969084; COSMIC: COSV59951506;