chr7-53138532-A-G

Variant names:

• chr7-53138532-A-G
• rs2330341

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 0.253 in 152,054 control chromosomes in the GnomAD database, including 5,034 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 0.25 (5034 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.878
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.326 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: 0.253 AC: 38507 AN: 151936 Hom.: 5044 Cov.: 33

Gnomad AFR AF: 0.198

Gnomad AMI AF: 0.293

Gnomad AMR AF: 0.328

Gnomad ASJ AF: 0.345

Gnomad EAS AF: 0.312

Gnomad SAS AF: 0.341

Gnomad FIN AF: 0.289

Gnomad MID AF: 0.405

Gnomad NFE AF: 0.248

Gnomad OTH AF: 0.286

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

GnomAD4 genome AF: 0.253 AC: 38509 AN: 152054 Hom.: 5034 Cov.: 33 AF XY: 0.261 AC XY: 19393 AN XY: 74326

African (AFR) AF: 0.197 AC: 8194 AN: 41502

American (AMR) AF: 0.328 AC: 4993 AN: 15238

Ashkenazi Jewish (ASJ) AF: 0.345 AC: 1196 AN: 3470

East Asian (EAS) AF: 0.312 AC: 1611 AN: 5170

South Asian (SAS) AF: 0.340 AC: 1638 AN: 4822

European-Finnish (FIN) AF: 0.289 AC: 3056 AN: 10570

Middle Eastern (MID) AF: 0.391 AC: 115 AN: 294

European-Non Finnish (NFE) AF: 0.248 AC: 16835 AN: 67970

Other (OTH) AF: 0.287 AC: 605 AN: 2110

Alfa AF: 0.255 Hom.: 12043

Bravo AF: 0.252

Asia WGS AF: 0.355 AC: 1234 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.72
DANN	Benign	0.65
PhyloP100		-0.88

Splicing

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

Other links and lift over

dbSNP: rs2330341; hg19: chr7-53206225;