12-65969290-T-G

Variant names:

• chr12-65969290-T-G
• rs7968902

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 0.546 in 152,088 control chromosomes in the GnomAD database, including 23,705 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 (23705 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.78
• Publications: 20 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.824 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: 0.547 AC: 83056 AN: 151970 Hom.: 23708 Cov.: 32

Gnomad AFR AF: 0.397

Gnomad AMI AF: 0.580

Gnomad AMR AF: 0.640

Gnomad ASJ AF: 0.702

Gnomad EAS AF: 0.846

Gnomad SAS AF: 0.726

Gnomad FIN AF: 0.578

Gnomad MID AF: 0.589

Gnomad NFE AF: 0.567

Gnomad OTH AF: 0.575

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

GnomAD4 genome AF: 0.546 AC: 83075 AN: 152088 Hom.: 23705 Cov.: 32 AF XY: 0.554 AC XY: 41187 AN XY: 74346

African (AFR) AF: 0.397 AC: 16457 AN: 41468

American (AMR) AF: 0.640 AC: 9780 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.702 AC: 2438 AN: 3472

East Asian (EAS) AF: 0.845 AC: 4377 AN: 5178

South Asian (SAS) AF: 0.725 AC: 3501 AN: 4826

European-Finnish (FIN) AF: 0.578 AC: 6118 AN: 10576

Middle Eastern (MID) AF: 0.575 AC: 169 AN: 294

European-Non Finnish (NFE) AF: 0.567 AC: 38504 AN: 67968

Other (OTH) AF: 0.571 AC: 1203 AN: 2108

Alfa AF: 0.565 Hom.: 69835

Bravo AF: 0.546

Asia WGS AF: 0.729 AC: 2534 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.12
DANN	Benign	0.66
PhyloP100		-1.8

Splicing

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

Other links and lift over

dbSNP: rs7968902; hg19: chr12-66363070;