rs1016988

Variant names:

• chr5-132408882-T-C
• rs1016988

Your query was ambiguous. Multiple possible variants found:

• chr5-132408882-T-C
• chr5-132408882-T-G

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 0.201 in 152,142 control chromosomes in the GnomAD database, including 3,305 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 0.20 (3305 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.223

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.71).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.377 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: 0.201 AC: 30534 AN: 152026 Hom.: 3305 Cov.: 33

Gnomad AFR AF: 0.149

Gnomad AMI AF: 0.102

Gnomad AMR AF: 0.179

Gnomad ASJ AF: 0.253

Gnomad EAS AF: 0.343

Gnomad SAS AF: 0.392

Gnomad FIN AF: 0.218

Gnomad MID AF: 0.304

Gnomad NFE AF: 0.208

Gnomad OTH AF: 0.206

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

GnomAD4 genome AF: 0.201 AC: 30548 AN: 152142 Hom.: 3305 Cov.: 33 AF XY: 0.206 AC XY: 15344 AN XY: 74366

Gnomad4 AFR AF: 0.149

Gnomad4 AMR AF: 0.180

Gnomad4 ASJ AF: 0.253

Gnomad4 EAS AF: 0.344

Gnomad4 SAS AF: 0.392

Gnomad4 FIN AF: 0.218

Gnomad4 NFE AF: 0.208

Gnomad4 OTH AF: 0.206

Alfa AF: 0.212 Hom.: 7671

Bravo AF: 0.192

Asia WGS AF: 0.356 AC: 1236 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.71
CADD	Benign	4.7
DANN	Benign	0.94

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1016988; hg19: chr5-131744574;