rs12704232

Positions:

• chr7-86172914-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 0.143 in 152,028 control chromosomes in the GnomAD database, including 1,661 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 0.14 (1661 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.370

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.16 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: 0.143 AC: 21746 AN: 151910 Hom.: 1662 Cov.: 32

Gnomad AFR AF: 0.164

Gnomad AMI AF: 0.197

Gnomad AMR AF: 0.145

Gnomad ASJ AF: 0.0805

Gnomad EAS AF: 0.0753

Gnomad SAS AF: 0.0536

Gnomad FIN AF: 0.225

Gnomad MID AF: 0.161

Gnomad NFE AF: 0.132

Gnomad OTH AF: 0.132

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

GnomAD4 genome AF: 0.143 AC: 21739 AN: 152028 Hom.: 1661 Cov.: 32 AF XY: 0.144 AC XY: 10694 AN XY: 74304

Gnomad4 AFR AF: 0.163

Gnomad4 AMR AF: 0.144

Gnomad4 ASJ AF: 0.0805

Gnomad4 EAS AF: 0.0760

Gnomad4 SAS AF: 0.0532

Gnomad4 FIN AF: 0.225

Gnomad4 NFE AF: 0.132

Gnomad4 OTH AF: 0.129

Alfa AF: 0.132 Hom.: 640

Bravo AF: 0.140

Asia WGS AF: 0.0780 AC: 270 AN: 3458

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.1
DANN	Benign	0.60

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12704232; hg19: chr7-85802230;