rs3863377

Positions:

• chr12-100472862-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The variant allele was found at a frequency of 0.0161 in 152,174 control chromosomes in the GnomAD database, including 25 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 0.016 (25 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.651

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BS1: Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.0161 (2444/152174) while in subpopulation NFE AF= 0.0248 (1687/68004). AF 95% confidence interval is 0.0238. There are 25 homozygotes in gnomad4. There are 1146 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd4 at 25 gene

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: 0.0161 AC: 2443 AN: 152056 Hom.: 25 Cov.: 32

Gnomad AFR AF: 0.00928

Gnomad AMI AF: 0.0143

Gnomad AMR AF: 0.0151

Gnomad ASJ AF: 0.00808

Gnomad EAS AF: 0.000386

Gnomad SAS AF: 0.00497

Gnomad FIN AF: 0.00490

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0248

Gnomad OTH AF: 0.0105

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

GnomAD4 genome AF: 0.0161 AC: 2444 AN: 152174 Hom.: 25 Cov.: 32 AF XY: 0.0154 AC XY: 1146 AN XY: 74386

Gnomad4 AFR AF: 0.00928

Gnomad4 AMR AF: 0.0151

Gnomad4 ASJ AF: 0.00808

Gnomad4 EAS AF: 0.000387

Gnomad4 SAS AF: 0.00498

Gnomad4 FIN AF: 0.00490

Gnomad4 NFE AF: 0.0248

Gnomad4 OTH AF: 0.0104

Alfa AF: 0.0221 Hom.: 3

Bravo AF: 0.0157

Asia WGS AF: 0.00289 AC: 10 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.28
DANN	Benign	0.57

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3863377; hg19: chr12-100866640;