12-109096844-T-C

Variant names:

• chr12-109096844-T-C
• rs2337395

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 0.55 in 151,744 control chromosomes in the GnomAD database, including 24,217 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 0.55 (24217 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.27

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.719 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: 0.550 AC: 83344 AN: 151626 Hom.: 24168 Cov.: 30

Gnomad AFR AF: 0.725

Gnomad AMI AF: 0.329

Gnomad AMR AF: 0.608

Gnomad ASJ AF: 0.465

Gnomad EAS AF: 0.722

Gnomad SAS AF: 0.510

Gnomad FIN AF: 0.498

Gnomad MID AF: 0.389

Gnomad NFE AF: 0.436

Gnomad OTH AF: 0.536

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

GnomAD4 genome AF: 0.550 AC: 83451 AN: 151744 Hom.: 24217 Cov.: 30 AF XY: 0.553 AC XY: 40991 AN XY: 74178

Gnomad4 AFR AF: 0.725

Gnomad4 AMR AF: 0.609

Gnomad4 ASJ AF: 0.465

Gnomad4 EAS AF: 0.722

Gnomad4 SAS AF: 0.508

Gnomad4 FIN AF: 0.498

Gnomad4 NFE AF: 0.436

Gnomad4 OTH AF: 0.538

Alfa AF: 0.503 Hom.: 2543

Bravo AF: 0.564

Asia WGS AF: 0.630 AC: 2190 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	1.7
DANN	Benign	0.28

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2337395; hg19: chr12-109534649;