1-200734413-C-T

Variant names:

• chr1-200734413-C-T
• rs6660197

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 0.129 in 152,040 control chromosomes in the GnomAD database, including 1,306 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 0.13 (1306 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.392
• Publications: 8 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.174 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: 0.129 AC: 19595 AN: 151922 Hom.: 1305 Cov.: 32

Gnomad AFR AF: 0.151

Gnomad AMI AF: 0.221

Gnomad AMR AF: 0.130

Gnomad ASJ AF: 0.0623

Gnomad EAS AF: 0.184

Gnomad SAS AF: 0.103

Gnomad FIN AF: 0.134

Gnomad MID AF: 0.0791

Gnomad NFE AF: 0.115

Gnomad OTH AF: 0.121

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

GnomAD4 genome AF: 0.129 AC: 19612 AN: 152040 Hom.: 1306 Cov.: 32 AF XY: 0.129 AC XY: 9599 AN XY: 74304

African (AFR) AF: 0.150 AC: 6231 AN: 41470

American (AMR) AF: 0.130 AC: 1991 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.0623 AC: 216 AN: 3468

East Asian (EAS) AF: 0.184 AC: 949 AN: 5164

South Asian (SAS) AF: 0.104 AC: 503 AN: 4824

European-Finnish (FIN) AF: 0.134 AC: 1416 AN: 10546

Middle Eastern (MID) AF: 0.0714 AC: 21 AN: 294

European-Non Finnish (NFE) AF: 0.115 AC: 7829 AN: 67982

Other (OTH) AF: 0.120 AC: 254 AN: 2110

Alfa AF: 0.112 Hom.: 3191

Bravo AF: 0.132

Asia WGS AF: 0.147 AC: 510 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	8.6
DANN	Benign	0.57
PhyloP100		0.39

Splicing

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

Other links and lift over

dbSNP: rs6660197; hg19: chr1-200703541;