chr5-116714628-T-A

Variant names:

• chr5-116714628-T-A
• rs10519480

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 0.0556 in 152,236 control chromosomes in the GnomAD database, including 672 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 0.056 (672 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.374

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.171 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: 0.0554 AC: 8430 AN: 152118 Hom.: 671 Cov.: 32

Gnomad AFR AF: 0.174

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0247

Gnomad ASJ AF: 0.00173

Gnomad EAS AF: 0.000770

Gnomad SAS AF: 0.0224

Gnomad FIN AF: 0.00640

Gnomad MID AF: 0.0253

Gnomad NFE AF: 0.00784

Gnomad OTH AF: 0.0507

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

GnomAD4 genome AF: 0.0556 AC: 8460 AN: 152236 Hom.: 672 Cov.: 32 AF XY: 0.0543 AC XY: 4040 AN XY: 74446

Gnomad4 AFR AF: 0.175

Gnomad4 AMR AF: 0.0247

Gnomad4 ASJ AF: 0.00173

Gnomad4 EAS AF: 0.000772

Gnomad4 SAS AF: 0.0222

Gnomad4 FIN AF: 0.00640

Gnomad4 NFE AF: 0.00784

Gnomad4 OTH AF: 0.0521

Alfa AF: 0.0331 Hom.: 47

Bravo AF: 0.0620

Asia WGS AF: 0.0250 AC: 87 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	1.2
DANN	Benign	0.44

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10519480; hg19: chr5-116050324;