1-24480070-T-C

Variant names:

• chr1-24480070-T-C
• rs195738

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 0.241 in 146,342 control chromosomes in the GnomAD database, including 6,456 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 0.24 (6456 hom., cov: 28)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.26
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.325 is higher than 0.05.

Variant Effect in Transcripts

 

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
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.241 AC: 35306 AN: 146224 Hom.: 6447 Cov.: 28

Gnomad AFR AF: 0.238

Gnomad AMI AF: 0.213

Gnomad AMR AF: 0.220

Gnomad ASJ AF: 0.167

Gnomad EAS AF: 0.338

Gnomad SAS AF: 0.277

Gnomad FIN AF: 0.301

Gnomad MID AF: 0.200

Gnomad NFE AF: 0.234

Gnomad OTH AF: 0.239

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

GnomAD4 genome AF: 0.241 AC: 35338 AN: 146342 Hom.: 6456 Cov.: 28 AF XY: 0.245 AC XY: 17408 AN XY: 71198

African (AFR) AF: 0.237 AC: 9288 AN: 39136

American (AMR) AF: 0.219 AC: 3217 AN: 14668

Ashkenazi Jewish (ASJ) AF: 0.167 AC: 557 AN: 3340

East Asian (EAS) AF: 0.339 AC: 1660 AN: 4900

South Asian (SAS) AF: 0.278 AC: 1239 AN: 4450

European-Finnish (FIN) AF: 0.301 AC: 3067 AN: 10176

Middle Eastern (MID) AF: 0.198 AC: 57 AN: 288

European-Non Finnish (NFE) AF: 0.234 AC: 15568 AN: 66492

Other (OTH) AF: 0.247 AC: 497 AN: 2010

Alfa AF: 0.239 Hom.: 5804

Asia WGS AF: 0.394 AC: 1335 AN: 3400

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.40
DANN	Benign	0.21
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs195738; hg19: chr1-24806560;