rs7721458

Variant names:

• chr5-143483675-C-A
• rs7721458

Your query was ambiguous. Multiple possible variants found:

• chr5-143483675-C-A
• chr5-143483675-C-G
• chr5-143483675-C-T

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 0.135 in 151,362 control chromosomes in the GnomAD database, including 2,474 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 0.14 (2474 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0970

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.29 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: 0.135 AC: 20413 AN: 151244 Hom.: 2469 Cov.: 32

Gnomad AFR AF: 0.295

Gnomad AMI AF: 0.0639

Gnomad AMR AF: 0.196

Gnomad ASJ AF: 0.0854

Gnomad EAS AF: 0.0720

Gnomad SAS AF: 0.131

Gnomad FIN AF: 0.0398

Gnomad MID AF: 0.156

Gnomad NFE AF: 0.0475

Gnomad OTH AF: 0.128

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

GnomAD4 genome AF: 0.135 AC: 20446 AN: 151362 Hom.: 2474 Cov.: 32 AF XY: 0.136 AC XY: 10061 AN XY: 73906

Gnomad4 AFR AF: 0.295

Gnomad4 AMR AF: 0.197

Gnomad4 ASJ AF: 0.0854

Gnomad4 EAS AF: 0.0720

Gnomad4 SAS AF: 0.131

Gnomad4 FIN AF: 0.0398

Gnomad4 NFE AF: 0.0474

Gnomad4 OTH AF: 0.126

Alfa AF: 0.00320 Hom.: 846

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	1.2
DANN	Benign	0.65

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7721458; hg19: chr5-142863240;