rs12704232

Variant names:

• chr7-86172914-A-G
• rs12704232

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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;