rs7728043

Variant names:

• chr5-5897581-T-C
• rs7728043

Your query was ambiguous. Multiple possible variants found:

• chr5-5897581-T-C
• chr5-5897581-T-G

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 0.454 in 151,784 control chromosomes in the GnomAD database, including 15,957 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 (15957 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.475
• Publications: 10 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.513 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: 0.454 AC: 68916 AN: 151666 Hom.: 15936 Cov.: 32

Gnomad AFR AF: 0.519

Gnomad AMI AF: 0.461

Gnomad AMR AF: 0.380

Gnomad ASJ AF: 0.411

Gnomad EAS AF: 0.465

Gnomad SAS AF: 0.341

Gnomad FIN AF: 0.400

Gnomad MID AF: 0.342

Gnomad NFE AF: 0.451

Gnomad OTH AF: 0.413

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

GnomAD4 genome AF: 0.454 AC: 68974 AN: 151784 Hom.: 15957 Cov.: 32 AF XY: 0.449 AC XY: 33266 AN XY: 74152

African (AFR) AF: 0.519 AC: 21463 AN: 41332

American (AMR) AF: 0.380 AC: 5792 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.411 AC: 1427 AN: 3472

East Asian (EAS) AF: 0.465 AC: 2391 AN: 5138

South Asian (SAS) AF: 0.341 AC: 1645 AN: 4818

European-Finnish (FIN) AF: 0.400 AC: 4208 AN: 10510

Middle Eastern (MID) AF: 0.330 AC: 97 AN: 294

European-Non Finnish (NFE) AF: 0.451 AC: 30660 AN: 67950

Other (OTH) AF: 0.412 AC: 872 AN: 2114

Alfa AF: 0.451 Hom.: 37597

Bravo AF: 0.457

Asia WGS AF: 0.419 AC: 1458 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.41
DANN	Benign	0.71
PhyloP100		-0.47

Splicing

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

Other links and lift over

dbSNP: rs7728043; hg19: chr5-5897694;