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. The variant received -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
• Publications: 46 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.149 AC: 6182 AN: 41496

American (AMR) AF: 0.180 AC: 2748 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.253 AC: 878 AN: 3472

East Asian (EAS) AF: 0.344 AC: 1783 AN: 5178

South Asian (SAS) AF: 0.392 AC: 1890 AN: 4824

European-Finnish (FIN) AF: 0.218 AC: 2307 AN: 10572

Middle Eastern (MID) AF: 0.296 AC: 87 AN: 294

European-Non Finnish (NFE) AF: 0.208 AC: 14144 AN: 67988

Other (OTH) AF: 0.206 AC: 436 AN: 2114

Alfa AF: 0.208 Hom.: 14733

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
PhyloP100		0.22

Splicing

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

Other links and lift over

dbSNP: rs1016988; hg19: chr5-131744574;