1-21496799-C-T

Position:

• chr1-21496799-C-T

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

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

Gnomad4 AFR AF: 0.131

Gnomad4 AMR AF: 0.500

Gnomad4 ASJ AF: 0.534

Gnomad4 EAS AF: 0.508

Gnomad4 SAS AF: 0.465

Gnomad4 FIN AF: 0.487

Gnomad4 NFE AF: 0.517

Gnomad4 OTH AF: 0.452

Alfa AF: 0.503 Hom.: 44170

Bravo AF: 0.393

Asia WGS AF: 0.427 AC: 1485 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1697421; hg19: chr1-21823292;