rs12407335

Variant names:

• chr1-106756963-G-A
• rs12407335

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 0.164 in 151,850 control chromosomes in the GnomAD database, including 2,261 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 (2261 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0550
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.272 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: 24807 AN: 151732 Hom.: 2254 Cov.: 31

Gnomad AFR AF: 0.209

Gnomad AMI AF: 0.198

Gnomad AMR AF: 0.151

Gnomad ASJ AF: 0.0762

Gnomad EAS AF: 0.284

Gnomad SAS AF: 0.193

Gnomad FIN AF: 0.147

Gnomad MID AF: 0.123

Gnomad NFE AF: 0.134

Gnomad OTH AF: 0.151

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

GnomAD4 genome AF: 0.164 AC: 24836 AN: 151850 Hom.: 2261 Cov.: 31 AF XY: 0.164 AC XY: 12165 AN XY: 74206

African (AFR) AF: 0.209 AC: 8663 AN: 41408

American (AMR) AF: 0.151 AC: 2306 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.0762 AC: 264 AN: 3464

East Asian (EAS) AF: 0.284 AC: 1455 AN: 5120

South Asian (SAS) AF: 0.192 AC: 926 AN: 4814

European-Finnish (FIN) AF: 0.147 AC: 1557 AN: 10556

Middle Eastern (MID) AF: 0.116 AC: 34 AN: 294

European-Non Finnish (NFE) AF: 0.134 AC: 9133 AN: 67922

Other (OTH) AF: 0.151 AC: 318 AN: 2108

Alfa AF: 0.153 Hom.: 309

Bravo AF: 0.170

Asia WGS AF: 0.241 AC: 840 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	1.3
DANN	Benign	0.59
PhyloP100		-0.055

Splicing

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

Other links and lift over

dbSNP: rs12407335; hg19: chr1-107299585;