rs7965364

Positions:

• chr12-25331259-C-T

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 0.705 in 152,128 control chromosomes in the GnomAD database, including 41,396 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 0.70 (41396 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.31

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.855 is higher than 0.05.

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: 0.705 AC: 107185 AN: 152010 Hom.: 41405 Cov.: 32

Gnomad AFR AF: 0.361

Gnomad AMI AF: 0.952

Gnomad AMR AF: 0.761

Gnomad ASJ AF: 0.805

Gnomad EAS AF: 0.756

Gnomad SAS AF: 0.675

Gnomad FIN AF: 0.895

Gnomad MID AF: 0.753

Gnomad NFE AF: 0.861

Gnomad OTH AF: 0.728

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

GnomAD4 genome AF: 0.705 AC: 107185 AN: 152128 Hom.: 41396 Cov.: 32 AF XY: 0.705 AC XY: 52454 AN XY: 74386

Gnomad4 AFR AF: 0.360

Gnomad4 AMR AF: 0.761

Gnomad4 ASJ AF: 0.805

Gnomad4 EAS AF: 0.756

Gnomad4 SAS AF: 0.674

Gnomad4 FIN AF: 0.895

Gnomad4 NFE AF: 0.861

Gnomad4 OTH AF: 0.725

Alfa AF: 0.758 Hom.: 5982

Bravo AF: 0.681

Asia WGS AF: 0.651 AC: 2266 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.48
DANN	Benign	0.56

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7965364; hg19: chr12-25484193;