7-145565315-A-G

Variant names:

• chr7-145565315-A-G
• rs2056553

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 0.455 in 151,924 control chromosomes in the GnomAD database, including 15,864 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 0.45 (15864 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.357

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.537 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: 0.455 AC: 69050 AN: 151806 Hom.: 15844 Cov.: 32

Gnomad AFR AF: 0.391

Gnomad AMI AF: 0.370

Gnomad AMR AF: 0.458

Gnomad ASJ AF: 0.494

Gnomad EAS AF: 0.486

Gnomad SAS AF: 0.554

Gnomad FIN AF: 0.441

Gnomad MID AF: 0.421

Gnomad NFE AF: 0.484

Gnomad OTH AF: 0.469

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

GnomAD4 genome AF: 0.455 AC: 69115 AN: 151924 Hom.: 15864 Cov.: 32 AF XY: 0.457 AC XY: 33897 AN XY: 74224

Gnomad4 AFR AF: 0.392

Gnomad4 AMR AF: 0.458

Gnomad4 ASJ AF: 0.494

Gnomad4 EAS AF: 0.486

Gnomad4 SAS AF: 0.554

Gnomad4 FIN AF: 0.441

Gnomad4 NFE AF: 0.484

Gnomad4 OTH AF: 0.469

Alfa AF: 0.365 Hom.: 1379

Bravo AF: 0.449

Asia WGS AF: 0.534 AC: 1857 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	2.6
DANN	Benign	0.42

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2056553; hg19: chr7-145262408;