12-96190080-G-A

Position:

• chr12-96190080-G-A

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BS1 BS2

The variant allele was found at a frequency of 0.0175 in 152,286 control chromosomes in the GnomAD database, including 34 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 0.018 (34 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.90

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.45).
• BS1: Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.0175 (2666/152286) while in subpopulation NFE AF= 0.0273 (1857/68016). AF 95% confidence interval is 0.0263. There are 34 homozygotes in gnomad4. There are 1238 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd4 at 34 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: 0.0175 AC: 2668 AN: 152168 Hom.: 34 Cov.: 32

Gnomad AFR AF: 0.00596

Gnomad AMI AF: 0.0877

Gnomad AMR AF: 0.0154

Gnomad ASJ AF: 0.0132

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00871

Gnomad FIN AF: 0.0100

Gnomad MID AF: 0.0348

Gnomad NFE AF: 0.0273

Gnomad OTH AF: 0.0211

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

GnomAD4 genome AF: 0.0175 AC: 2666 AN: 152286 Hom.: 34 Cov.: 32 AF XY: 0.0166 AC XY: 1238 AN XY: 74450

Gnomad4 AFR AF: 0.00594

Gnomad4 AMR AF: 0.0153

Gnomad4 ASJ AF: 0.0132

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00871

Gnomad4 FIN AF: 0.0100

Gnomad4 NFE AF: 0.0273

Gnomad4 OTH AF: 0.0209

Alfa AF: 0.0207 Hom.: 3

Bravo AF: 0.0183

Asia WGS AF: 0.00664 AC: 23 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.45
CADD	Benign	8.5
DANN	Benign	0.59

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs61938844; hg19: chr12-96583858;