rs1358503

Variant names:

• chr7-80969826-T-C
• rs1358503

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 0.455 in 152,008 control chromosomes in the GnomAD database, including 16,360 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 (16360 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.747

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.537 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: 0.455 AC: 69085 AN: 151888 Hom.: 16350 Cov.: 31

Gnomad AFR AF: 0.362

Gnomad AMI AF: 0.491

Gnomad AMR AF: 0.546

Gnomad ASJ AF: 0.572

Gnomad EAS AF: 0.229

Gnomad SAS AF: 0.515

Gnomad FIN AF: 0.411

Gnomad MID AF: 0.529

Gnomad NFE AF: 0.503

Gnomad OTH AF: 0.484

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

GnomAD4 genome AF: 0.455 AC: 69133 AN: 152008 Hom.: 16360 Cov.: 31 AF XY: 0.451 AC XY: 33493 AN XY: 74324

Gnomad4 AFR AF: 0.362

Gnomad4 AMR AF: 0.547

Gnomad4 ASJ AF: 0.572

Gnomad4 EAS AF: 0.229

Gnomad4 SAS AF: 0.515

Gnomad4 FIN AF: 0.411

Gnomad4 NFE AF: 0.503

Gnomad4 OTH AF: 0.484

Alfa AF: 0.502 Hom.: 39927

Bravo AF: 0.458

Asia WGS AF: 0.402 AC: 1397 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.3
DANN	Benign	0.37

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1358503; hg19: chr7-80599142;