rs12671457

Variant names:

• chr7-45907327-A-C
• rs12671457

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 0.116 in 152,212 control chromosomes in the GnomAD database, including 1,198 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 0.12 (1198 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.981
• Publications: 7 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.172 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: 0.116 AC: 17681 AN: 152094 Hom.: 1200 Cov.: 32

Gnomad AFR AF: 0.0443

Gnomad AMI AF: 0.0384

Gnomad AMR AF: 0.0874

Gnomad ASJ AF: 0.215

Gnomad EAS AF: 0.183

Gnomad SAS AF: 0.0532

Gnomad FIN AF: 0.178

Gnomad MID AF: 0.0601

Gnomad NFE AF: 0.152

Gnomad OTH AF: 0.131

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

GnomAD4 genome AF: 0.116 AC: 17683 AN: 152212 Hom.: 1198 Cov.: 32 AF XY: 0.115 AC XY: 8572 AN XY: 74412

African (AFR) AF: 0.0443 AC: 1842 AN: 41548

American (AMR) AF: 0.0872 AC: 1334 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.215 AC: 746 AN: 3466

East Asian (EAS) AF: 0.182 AC: 943 AN: 5186

South Asian (SAS) AF: 0.0535 AC: 258 AN: 4824

European-Finnish (FIN) AF: 0.178 AC: 1887 AN: 10594

Middle Eastern (MID) AF: 0.0612 AC: 18 AN: 294

European-Non Finnish (NFE) AF: 0.152 AC: 10341 AN: 67988

Other (OTH) AF: 0.132 AC: 279 AN: 2110

Alfa AF: 0.138 Hom.: 1146

Bravo AF: 0.108

Asia WGS AF: 0.0970 AC: 335 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	4.9
DANN	Benign	0.70
PhyloP100		-0.98

Splicing

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

Other links and lift over

dbSNP: rs12671457; hg19: chr7-45946926;