chr1-24966593-T-C

Variant names:

• chr1-24966593-T-C
• rs7536201

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 0.48 in 150,518 control chromosomes in the GnomAD database, including 18,507 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 0.48 (18507 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.244
• Publications: 31 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.693 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.480 AC: 72168 AN: 150394 Hom.: 18479 Cov.: 32

Gnomad AFR AF: 0.292

Gnomad AMI AF: 0.694

Gnomad AMR AF: 0.641

Gnomad ASJ AF: 0.512

Gnomad EAS AF: 0.713

Gnomad SAS AF: 0.675

Gnomad FIN AF: 0.589

Gnomad MID AF: 0.535

Gnomad NFE AF: 0.503

Gnomad OTH AF: 0.514

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

GnomAD4 genome AF: 0.480 AC: 72215 AN: 150518 Hom.: 18507 Cov.: 32 AF XY: 0.495 AC XY: 36423 AN XY: 73526

African (AFR) AF: 0.291 AC: 11882 AN: 40778

American (AMR) AF: 0.642 AC: 9778 AN: 15236

Ashkenazi Jewish (ASJ) AF: 0.512 AC: 1765 AN: 3450

East Asian (EAS) AF: 0.712 AC: 3639 AN: 5110

South Asian (SAS) AF: 0.675 AC: 3229 AN: 4784

European-Finnish (FIN) AF: 0.589 AC: 6057 AN: 10288

Middle Eastern (MID) AF: 0.537 AC: 158 AN: 294

European-Non Finnish (NFE) AF: 0.503 AC: 33994 AN: 67582

Other (OTH) AF: 0.519 AC: 1086 AN: 2092

Alfa AF: 0.279 Hom.: 643

Bravo AF: 0.472

Asia WGS AF: 0.691 AC: 2403 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.6
DANN	Benign	0.59
PhyloP100		-0.24

Splicing

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

Other links and lift over

dbSNP: rs7536201; hg19: chr1-25293084;