1-216459606-T-C

Variant names:

• chr1-216459606-T-C
• rs10495024

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 0.324 in 152,036 control chromosomes in the GnomAD database, including 8,310 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 0.32 (8310 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.831
• Publications: 8 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.488 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: 0.324 AC: 49238 AN: 151918 Hom.: 8311 Cov.: 32

Gnomad AFR AF: 0.248

Gnomad AMI AF: 0.507

Gnomad AMR AF: 0.351

Gnomad ASJ AF: 0.263

Gnomad EAS AF: 0.505

Gnomad SAS AF: 0.269

Gnomad FIN AF: 0.394

Gnomad MID AF: 0.244

Gnomad NFE AF: 0.345

Gnomad OTH AF: 0.313

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

GnomAD4 genome AF: 0.324 AC: 49249 AN: 152036 Hom.: 8310 Cov.: 32 AF XY: 0.328 AC XY: 24397 AN XY: 74320

African (AFR) AF: 0.248 AC: 10261 AN: 41456

American (AMR) AF: 0.352 AC: 5368 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.263 AC: 912 AN: 3472

East Asian (EAS) AF: 0.504 AC: 2605 AN: 5166

South Asian (SAS) AF: 0.269 AC: 1299 AN: 4822

European-Finnish (FIN) AF: 0.394 AC: 4161 AN: 10566

Middle Eastern (MID) AF: 0.238 AC: 70 AN: 294

European-Non Finnish (NFE) AF: 0.345 AC: 23461 AN: 67970

Other (OTH) AF: 0.309 AC: 651 AN: 2110

Alfa AF: 0.326 Hom.: 27193

Bravo AF: 0.321

Asia WGS AF: 0.350 AC: 1218 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	6.8
DANN	Benign	0.45
PhyloP100		0.83

Splicing

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

Other links and lift over

dbSNP: rs10495024; hg19: chr1-216632948; COSMIC: COSV69337617;