7-145565315-A-G

Variant names:

• chr7-145565315-A-G
• rs2056553

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 0.455 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
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.392 AC: 16228 AN: 41426

American (AMR) AF: 0.458 AC: 6990 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.494 AC: 1712 AN: 3464

East Asian (EAS) AF: 0.486 AC: 2505 AN: 5158

South Asian (SAS) AF: 0.554 AC: 2666 AN: 4808

European-Finnish (FIN) AF: 0.441 AC: 4655 AN: 10548

Middle Eastern (MID) AF: 0.442 AC: 130 AN: 294

European-Non Finnish (NFE) AF: 0.484 AC: 32904 AN: 67962

Other (OTH) AF: 0.469 AC: 989 AN: 2108

Alfa AF: 0.366 Hom.: 1429

Bravo AF: 0.449

Asia WGS AF: 0.534 AC: 1857 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.6
DANN	Benign	0.42
PhyloP100		-0.36

Splicing

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

Other links and lift over

dbSNP: rs2056553; hg19: chr7-145262408;