chr12-91101386-G-A

Variant names:

• chr12-91101386-G-A
• rs17714469

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 0.0785 in 152,102 control chromosomes in the GnomAD database, including 585 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 0.078 (585 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.50
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.11 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: 0.0785 AC: 11925 AN: 151984 Hom.: 583 Cov.: 32

Gnomad AFR AF: 0.0321

Gnomad AMI AF: 0.126

Gnomad AMR AF: 0.0899

Gnomad ASJ AF: 0.0989

Gnomad EAS AF: 0.00115

Gnomad SAS AF: 0.0404

Gnomad FIN AF: 0.0726

Gnomad MID AF: 0.0759

Gnomad NFE AF: 0.112

Gnomad OTH AF: 0.0906

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

GnomAD4 genome AF: 0.0785 AC: 11933 AN: 152102 Hom.: 585 Cov.: 32 AF XY: 0.0773 AC XY: 5743 AN XY: 74342

African (AFR) AF: 0.0321 AC: 1335 AN: 41546

American (AMR) AF: 0.0902 AC: 1374 AN: 15232

Ashkenazi Jewish (ASJ) AF: 0.0989 AC: 343 AN: 3468

East Asian (EAS) AF: 0.00116 AC: 6 AN: 5184

South Asian (SAS) AF: 0.0408 AC: 197 AN: 4828

European-Finnish (FIN) AF: 0.0726 AC: 769 AN: 10596

Middle Eastern (MID) AF: 0.0714 AC: 21 AN: 294

European-Non Finnish (NFE) AF: 0.112 AC: 7583 AN: 67936

Other (OTH) AF: 0.0901 AC: 190 AN: 2108

Alfa AF: 0.0920 Hom.: 94

Bravo AF: 0.0775

Asia WGS AF: 0.0240 AC: 84 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.49
DANN	Benign	0.33
PhyloP100		-1.5

Splicing

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

Other links and lift over

dbSNP: rs17714469; hg19: chr12-91495163; COSMIC: COSV57128351;