rs3007729

Variant names:

• chr1-18468761-T-C
• rs3007729

Your query was ambiguous. Multiple possible variants found:

• chr1-18468761-T-C
• chr1-18468761-T-G

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 0.393 in 152,018 control chromosomes in the GnomAD database, including 11,979 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 0.39 (11979 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.33
• Publications: 19 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.616 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: 0.393 AC: 59670 AN: 151900 Hom.: 11966 Cov.: 32

Gnomad AFR AF: 0.427

Gnomad AMI AF: 0.409

Gnomad AMR AF: 0.365

Gnomad ASJ AF: 0.259

Gnomad EAS AF: 0.635

Gnomad SAS AF: 0.378

Gnomad FIN AF: 0.408

Gnomad MID AF: 0.256

Gnomad NFE AF: 0.366

Gnomad OTH AF: 0.377

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

GnomAD4 genome AF: 0.393 AC: 59723 AN: 152018 Hom.: 11979 Cov.: 32 AF XY: 0.396 AC XY: 29452 AN XY: 74292

African (AFR) AF: 0.428 AC: 17728 AN: 41456

American (AMR) AF: 0.365 AC: 5576 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.259 AC: 899 AN: 3472

East Asian (EAS) AF: 0.634 AC: 3265 AN: 5146

South Asian (SAS) AF: 0.379 AC: 1826 AN: 4820

European-Finnish (FIN) AF: 0.408 AC: 4312 AN: 10568

Middle Eastern (MID) AF: 0.241 AC: 71 AN: 294

European-Non Finnish (NFE) AF: 0.366 AC: 24883 AN: 67970

Other (OTH) AF: 0.375 AC: 790 AN: 2106

Alfa AF: 0.368 Hom.: 37175

Bravo AF: 0.393

Asia WGS AF: 0.484 AC: 1681 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.36
DANN	Benign	0.35
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs3007729; hg19: chr1-18795255;