1-9275686-C-T

Variant names:

• chr1-9275686-C-T
• rs6688233

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 0.192 in 151,954 control chromosomes in the GnomAD database, including 3,099 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 (3099 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00
• Publications: 16 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.242 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: 0.192 AC: 29135 AN: 151836 Hom.: 3098 Cov.: 32

Gnomad AFR AF: 0.103

Gnomad AMI AF: 0.194

Gnomad AMR AF: 0.194

Gnomad ASJ AF: 0.194

Gnomad EAS AF: 0.196

Gnomad SAS AF: 0.192

Gnomad FIN AF: 0.182

Gnomad MID AF: 0.269

Gnomad NFE AF: 0.246

Gnomad OTH AF: 0.222

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

GnomAD4 genome AF: 0.192 AC: 29137 AN: 151954 Hom.: 3099 Cov.: 32 AF XY: 0.188 AC XY: 13953 AN XY: 74264

African (AFR) AF: 0.103 AC: 4251 AN: 41454

American (AMR) AF: 0.194 AC: 2959 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.194 AC: 673 AN: 3466

East Asian (EAS) AF: 0.196 AC: 1014 AN: 5168

South Asian (SAS) AF: 0.192 AC: 923 AN: 4806

European-Finnish (FIN) AF: 0.182 AC: 1919 AN: 10564

Middle Eastern (MID) AF: 0.272 AC: 80 AN: 294

European-Non Finnish (NFE) AF: 0.246 AC: 16680 AN: 67920

Other (OTH) AF: 0.219 AC: 462 AN: 2106

Alfa AF: 0.221 Hom.: 6474

Bravo AF: 0.192

Asia WGS AF: 0.194 AC: 673 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	8.6
DANN	Benign	0.48
PhyloP100		0.0

Splicing

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

Other links and lift over

dbSNP: rs6688233; hg19: chr1-9335745;