rs1812607

Variant names:

• chr1-117710673-C-T
• rs1812607

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 0.163 in 152,276 control chromosomes in the GnomAD database, including 2,317 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 0.16 (2317 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.154
• Publications: 7 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.227 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: 0.163 AC: 24748 AN: 152158 Hom.: 2318 Cov.: 33

Gnomad AFR AF: 0.0631

Gnomad AMI AF: 0.189

Gnomad AMR AF: 0.234

Gnomad ASJ AF: 0.244

Gnomad EAS AF: 0.219

Gnomad SAS AF: 0.171

Gnomad FIN AF: 0.184

Gnomad MID AF: 0.158

Gnomad NFE AF: 0.194

Gnomad OTH AF: 0.177

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

GnomAD4 genome AF: 0.163 AC: 24750 AN: 152276 Hom.: 2317 Cov.: 33 AF XY: 0.166 AC XY: 12323 AN XY: 74432

African (AFR) AF: 0.0630 AC: 2619 AN: 41584

American (AMR) AF: 0.234 AC: 3577 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.244 AC: 846 AN: 3470

East Asian (EAS) AF: 0.219 AC: 1133 AN: 5176

South Asian (SAS) AF: 0.171 AC: 827 AN: 4828

European-Finnish (FIN) AF: 0.184 AC: 1952 AN: 10590

Middle Eastern (MID) AF: 0.156 AC: 46 AN: 294

European-Non Finnish (NFE) AF: 0.194 AC: 13207 AN: 68010

Other (OTH) AF: 0.176 AC: 371 AN: 2112

Alfa AF: 0.186 Hom.: 8184

Bravo AF: 0.165

Asia WGS AF: 0.179 AC: 620 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	4.8
DANN	Benign	0.58
PhyloP100		0.15

Splicing

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

Other links and lift over

dbSNP: rs1812607; hg19: chr1-118253295;