rs3007729

chr1-18468761-T-Cchr1-18468761-T-G

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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

Gnomad4 AFR AF: 0.428

Gnomad4 AMR AF: 0.365

Gnomad4 ASJ AF: 0.259

Gnomad4 EAS AF: 0.634

Gnomad4 SAS AF: 0.379

Gnomad4 FIN AF: 0.408

Gnomad4 NFE AF: 0.366

Gnomad4 OTH AF: 0.375

Alfa AF: 0.361 Hom.: 23000

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3007729; hg19: chr1-18795255;