rs1468915

Positions:

• chr7-12188266-A-G

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 0.198 in 152,072 control chromosomes in the GnomAD database, including 3,379 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 0.20 (3379 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.33

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.334 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.198 AC: 30053 AN: 151954 Hom.: 3384 Cov.: 32

Gnomad AFR AF: 0.0859

Gnomad AMI AF: 0.159

Gnomad AMR AF: 0.254

Gnomad ASJ AF: 0.239

Gnomad EAS AF: 0.347

Gnomad SAS AF: 0.333

Gnomad FIN AF: 0.206

Gnomad MID AF: 0.250

Gnomad NFE AF: 0.229

Gnomad OTH AF: 0.203

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

GnomAD4 genome AF: 0.198 AC: 30053 AN: 152072 Hom.: 3379 Cov.: 32 AF XY: 0.202 AC XY: 15018 AN XY: 74310

Gnomad4 AFR AF: 0.0858

Gnomad4 AMR AF: 0.254

Gnomad4 ASJ AF: 0.239

Gnomad4 EAS AF: 0.347

Gnomad4 SAS AF: 0.332

Gnomad4 FIN AF: 0.206

Gnomad4 NFE AF: 0.229

Gnomad4 OTH AF: 0.205

Alfa AF: 0.228 Hom.: 4935

Bravo AF: 0.192

Asia WGS AF: 0.312 AC: 1083 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	6.3
DANN	Benign	0.76

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1468915; hg19: chr7-12227892;