rs12533271

chr7-155465108-T-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The variant allele was found at a frequency of 0.0126 in 152,338 control chromosomes in the GnomAD database, including 40 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 0.013 (40 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.64

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BS1: Variant frequency is greater than expected in population amr. gnomad4 allele frequency = 0.0126 (1922/152338) while in subpopulation AMR AF= 0.0371 (568/15308). AF 95% confidence interval is 0.0346. There are 40 homozygotes in gnomad4. There are 951 alleles in male gnomad4 subpopulation. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd at 38 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.0126 AC: 1914 AN: 152220 Hom.: 38 Cov.: 33

Gnomad AFR AF: 0.00639

Gnomad AMI AF: 0.00110

Gnomad AMR AF: 0.0366

Gnomad ASJ AF: 0.0133

Gnomad EAS AF: 0.00846

Gnomad SAS AF: 0.0260

Gnomad FIN AF: 0.00179

Gnomad MID AF: 0.0127

Gnomad NFE AF: 0.0119

Gnomad OTH AF: 0.0201

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

GnomAD4 genome AF: 0.0126 AC: 1922 AN: 152338 Hom.: 40 Cov.: 33 AF XY: 0.0128 AC XY: 951 AN XY: 74490

Gnomad4 AFR AF: 0.00640

Gnomad4 AMR AF: 0.0371

Gnomad4 ASJ AF: 0.0133

Gnomad4 EAS AF: 0.00848

Gnomad4 SAS AF: 0.0260

Gnomad4 FIN AF: 0.00179

Gnomad4 NFE AF: 0.0119

Gnomad4 OTH AF: 0.0199

Alfa AF: 0.0121 Hom.: 7

Bravo AF: 0.0166

Asia WGS AF: 0.0210 AC: 72 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
Cadd	Benign	0.16
Dann	Benign	0.55

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12533271; hg19: chr7-155257803;