rs7723053

Variant names:

• chr5-3347611-T-C
• rs7723053

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 0.401 in 152,074 control chromosomes in the GnomAD database, including 12,626 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 0.40 (12626 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.40
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.482 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: 0.401 AC: 60912 AN: 151958 Hom.: 12612 Cov.: 33

Gnomad AFR AF: 0.488

Gnomad AMI AF: 0.222

Gnomad AMR AF: 0.440

Gnomad ASJ AF: 0.297

Gnomad EAS AF: 0.358

Gnomad SAS AF: 0.354

Gnomad FIN AF: 0.423

Gnomad MID AF: 0.427

Gnomad NFE AF: 0.350

Gnomad OTH AF: 0.384

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

GnomAD4 genome AF: 0.401 AC: 60964 AN: 152074 Hom.: 12626 Cov.: 33 AF XY: 0.405 AC XY: 30121 AN XY: 74346

African (AFR) AF: 0.488 AC: 20219 AN: 41474

American (AMR) AF: 0.441 AC: 6730 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.297 AC: 1029 AN: 3466

East Asian (EAS) AF: 0.358 AC: 1852 AN: 5170

South Asian (SAS) AF: 0.353 AC: 1704 AN: 4824

European-Finnish (FIN) AF: 0.423 AC: 4465 AN: 10564

Middle Eastern (MID) AF: 0.414 AC: 121 AN: 292

European-Non Finnish (NFE) AF: 0.351 AC: 23830 AN: 67984

Other (OTH) AF: 0.384 AC: 812 AN: 2112

Alfa AF: 0.398 Hom.: 2088

Bravo AF: 0.405

Asia WGS AF: 0.372 AC: 1296 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.11
DANN	Benign	0.42
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs7723053; hg19: chr5-3347725;