1-199870870-T-C

Variant names:

• chr1-199870870-T-C
• rs17664308

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 0.313 in 152,054 control chromosomes in the GnomAD database, including 8,749 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 0.31 (8749 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.928
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.72).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.572 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.313 AC: 47625 AN: 151936 Hom.: 8747 Cov.: 32

Gnomad AFR AF: 0.120

Gnomad AMI AF: 0.408

Gnomad AMR AF: 0.378

Gnomad ASJ AF: 0.315

Gnomad EAS AF: 0.589

Gnomad SAS AF: 0.480

Gnomad FIN AF: 0.467

Gnomad MID AF: 0.364

Gnomad NFE AF: 0.359

Gnomad OTH AF: 0.309

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

GnomAD4 genome AF: 0.313 AC: 47630 AN: 152054 Hom.: 8749 Cov.: 32 AF XY: 0.326 AC XY: 24210 AN XY: 74322

African (AFR) AF: 0.119 AC: 4956 AN: 41506

American (AMR) AF: 0.378 AC: 5770 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.315 AC: 1095 AN: 3472

East Asian (EAS) AF: 0.590 AC: 3047 AN: 5166

South Asian (SAS) AF: 0.482 AC: 2319 AN: 4814

European-Finnish (FIN) AF: 0.467 AC: 4931 AN: 10552

Middle Eastern (MID) AF: 0.354 AC: 104 AN: 294

European-Non Finnish (NFE) AF: 0.359 AC: 24390 AN: 67962

Other (OTH) AF: 0.307 AC: 647 AN: 2106

Alfa AF: 0.341 Hom.: 9734

Bravo AF: 0.294

Asia WGS AF: 0.477 AC: 1657 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.72
CADD	Benign	9.4
DANN	Benign	0.95
PhyloP100		-0.93

Splicing

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

Other links and lift over

dbSNP: rs17664308; hg19: chr1-199839998; COSMIC: COSV60016982;