rs12453544

Variant names:

• chr17-55330426-G-A
• rs12453544

Your query was ambiguous. Multiple possible variants found:

• chr17-55330426-G-A
• chr17-55330426-G-C

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 0.102 in 152,112 control chromosomes in the GnomAD database, including 1,066 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 0.10 (1066 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.84
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.68).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.144 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: 0.102 AC: 15544 AN: 151994 Hom.: 1065 Cov.: 32

Gnomad AFR AF: 0.0283

Gnomad AMI AF: 0.123

Gnomad AMR AF: 0.0945

Gnomad ASJ AF: 0.113

Gnomad EAS AF: 0.00424

Gnomad SAS AF: 0.0665

Gnomad FIN AF: 0.180

Gnomad MID AF: 0.0475

Gnomad NFE AF: 0.147

Gnomad OTH AF: 0.0893

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

GnomAD4 genome AF: 0.102 AC: 15549 AN: 152112 Hom.: 1066 Cov.: 32 AF XY: 0.102 AC XY: 7576 AN XY: 74364

African (AFR) AF: 0.0282 AC: 1173 AN: 41526

American (AMR) AF: 0.0945 AC: 1444 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.113 AC: 392 AN: 3468

East Asian (EAS) AF: 0.00425 AC: 22 AN: 5176

South Asian (SAS) AF: 0.0676 AC: 326 AN: 4824

European-Finnish (FIN) AF: 0.180 AC: 1903 AN: 10554

Middle Eastern (MID) AF: 0.0476 AC: 14 AN: 294

European-Non Finnish (NFE) AF: 0.147 AC: 9977 AN: 67968

Other (OTH) AF: 0.0879 AC: 186 AN: 2116

Alfa AF: 0.108 Hom.: 742

Bravo AF: 0.0942

Asia WGS AF: 0.0330 AC: 116 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.68
CADD	Benign	14
DANN	Benign	0.87
PhyloP100		1.8

Splicing

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

Other links and lift over

dbSNP: rs12453544; hg19: chr17-53407787;