chr7-131603231-C-A

Variant names:

• chr7-131603231-C-A
• rs12534221

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 0.134 in 152,136 control chromosomes in the GnomAD database, including 1,694 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 0.13 (1694 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.783

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.282 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: 0.134 AC: 20375 AN: 152018 Hom.: 1697 Cov.: 32

Gnomad AFR AF: 0.0509

Gnomad AMI AF: 0.0471

Gnomad AMR AF: 0.161

Gnomad ASJ AF: 0.159

Gnomad EAS AF: 0.295

Gnomad SAS AF: 0.162

Gnomad FIN AF: 0.206

Gnomad MID AF: 0.108

Gnomad NFE AF: 0.153

Gnomad OTH AF: 0.150

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

GnomAD4 genome AF: 0.134 AC: 20372 AN: 152136 Hom.: 1694 Cov.: 32 AF XY: 0.137 AC XY: 10223 AN XY: 74354

Gnomad4 AFR AF: 0.0508

Gnomad4 AMR AF: 0.161

Gnomad4 ASJ AF: 0.159

Gnomad4 EAS AF: 0.294

Gnomad4 SAS AF: 0.162

Gnomad4 FIN AF: 0.206

Gnomad4 NFE AF: 0.153

Gnomad4 OTH AF: 0.149

Alfa AF: 0.154 Hom.: 4274

Bravo AF: 0.129

Asia WGS AF: 0.214 AC: 740 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	6.0
DANN	Benign	0.58

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12534221; hg19: chr7-131287990;