1-21496799-C-T

Variant names:

• chr1-21496799-C-T
• rs1697421

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 0.406 in 152,064 control chromosomes in the GnomAD database, including 14,810 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 0.41 (14810 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.367
• Publications: 47 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.513 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: 0.406 AC: 61697 AN: 151946 Hom.: 14811 Cov.: 32

Gnomad AFR AF: 0.132

Gnomad AMI AF: 0.520

Gnomad AMR AF: 0.500

Gnomad ASJ AF: 0.534

Gnomad EAS AF: 0.508

Gnomad SAS AF: 0.463

Gnomad FIN AF: 0.487

Gnomad MID AF: 0.601

Gnomad NFE AF: 0.517

Gnomad OTH AF: 0.456

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

GnomAD4 genome AF: 0.406 AC: 61691 AN: 152064 Hom.: 14810 Cov.: 32 AF XY: 0.409 AC XY: 30389 AN XY: 74314

African (AFR) AF: 0.131 AC: 5446 AN: 41494

American (AMR) AF: 0.500 AC: 7643 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.534 AC: 1850 AN: 3464

East Asian (EAS) AF: 0.508 AC: 2634 AN: 5180

South Asian (SAS) AF: 0.465 AC: 2238 AN: 4812

European-Finnish (FIN) AF: 0.487 AC: 5141 AN: 10550

Middle Eastern (MID) AF: 0.585 AC: 172 AN: 294

European-Non Finnish (NFE) AF: 0.517 AC: 35142 AN: 67968

Other (OTH) AF: 0.452 AC: 952 AN: 2108

Alfa AF: 0.484 Hom.: 85572

Bravo AF: 0.393

Asia WGS AF: 0.427 AC: 1485 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	2.0
DANN	Benign	0.31
PhyloP100		0.37

Splicing

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

Other links and lift over

dbSNP: rs1697421; hg19: chr1-21823292;