1-200016664-C-T

Variant names:

• chr1-200016664-C-T
• rs2821347

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 0.194 in 152,046 control chromosomes in the GnomAD database, including 3,572 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 0.19 (3572 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.41
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.344 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.194 AC: 29401 AN: 151928 Hom.: 3561 Cov.: 32

Gnomad AFR AF: 0.348

Gnomad AMI AF: 0.143

Gnomad AMR AF: 0.128

Gnomad ASJ AF: 0.123

Gnomad EAS AF: 0.0294

Gnomad SAS AF: 0.0795

Gnomad FIN AF: 0.121

Gnomad MID AF: 0.139

Gnomad NFE AF: 0.151

Gnomad OTH AF: 0.187

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

GnomAD4 genome AF: 0.194 AC: 29450 AN: 152046 Hom.: 3572 Cov.: 32 AF XY: 0.188 AC XY: 13955 AN XY: 74324

African (AFR) AF: 0.348 AC: 14426 AN: 41422

American (AMR) AF: 0.128 AC: 1948 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.123 AC: 428 AN: 3470

East Asian (EAS) AF: 0.0295 AC: 153 AN: 5188

South Asian (SAS) AF: 0.0798 AC: 385 AN: 4824

European-Finnish (FIN) AF: 0.121 AC: 1284 AN: 10572

Middle Eastern (MID) AF: 0.146 AC: 43 AN: 294

European-Non Finnish (NFE) AF: 0.151 AC: 10260 AN: 67992

Other (OTH) AF: 0.186 AC: 393 AN: 2114

Alfa AF: 0.140 Hom.: 1004

Bravo AF: 0.200

Asia WGS AF: 0.0800 AC: 281 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.068
DANN	Benign	0.48
PhyloP100		-3.4

Splicing

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

Other links and lift over

dbSNP: rs2821347; hg19: chr1-199985792;