12-107872108-C-T

Variant names:

• chr12-107872108-C-T
• rs7311236

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 0.797 in 152,146 control chromosomes in the GnomAD database, including 48,449 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 0.80 (48449 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.221
• Publications: 5 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 (AFR) allele frequency at 95% confidence interval = 0.816 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: 0.797 AC: 121114 AN: 152028 Hom.: 48403 Cov.: 31

Gnomad AFR AF: 0.823

Gnomad AMI AF: 0.815

Gnomad AMR AF: 0.804

Gnomad ASJ AF: 0.750

Gnomad EAS AF: 0.587

Gnomad SAS AF: 0.657

Gnomad FIN AF: 0.763

Gnomad MID AF: 0.744

Gnomad NFE AF: 0.813

Gnomad OTH AF: 0.774

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

GnomAD4 genome AF: 0.797 AC: 121215 AN: 152146 Hom.: 48449 Cov.: 31 AF XY: 0.791 AC XY: 58842 AN XY: 74358

African (AFR) AF: 0.823 AC: 34175 AN: 41518

American (AMR) AF: 0.805 AC: 12311 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.750 AC: 2601 AN: 3468

East Asian (EAS) AF: 0.587 AC: 3033 AN: 5164

South Asian (SAS) AF: 0.657 AC: 3165 AN: 4818

European-Finnish (FIN) AF: 0.763 AC: 8059 AN: 10564

Middle Eastern (MID) AF: 0.745 AC: 219 AN: 294

European-Non Finnish (NFE) AF: 0.813 AC: 55284 AN: 67998

Other (OTH) AF: 0.769 AC: 1625 AN: 2112

Alfa AF: 0.758 Hom.: 2571

Bravo AF: 0.803

Asia WGS AF: 0.620 AC: 2157 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	2.5
DANN	Benign	0.67
PhyloP100		-0.22

Splicing

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

Other links and lift over

dbSNP: rs7311236; hg19: chr12-108265885;