rs2112416

Variant names:

• chr5-80885328-T-A
• rs2112416

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 0.156 in 152,146 control chromosomes in the GnomAD database, including 2,098 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 0.16 (2098 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.353
• Publications: 5 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.72).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.347 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: 0.156 AC: 23648 AN: 152030 Hom.: 2092 Cov.: 32

Gnomad AFR AF: 0.142

Gnomad AMI AF: 0.181

Gnomad AMR AF: 0.236

Gnomad ASJ AF: 0.187

Gnomad EAS AF: 0.361

Gnomad SAS AF: 0.178

Gnomad FIN AF: 0.112

Gnomad MID AF: 0.142

Gnomad NFE AF: 0.134

Gnomad OTH AF: 0.158

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

GnomAD4 genome AF: 0.156 AC: 23693 AN: 152146 Hom.: 2098 Cov.: 32 AF XY: 0.158 AC XY: 11717 AN XY: 74380

African (AFR) AF: 0.142 AC: 5898 AN: 41530

American (AMR) AF: 0.236 AC: 3603 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.187 AC: 649 AN: 3468

East Asian (EAS) AF: 0.361 AC: 1858 AN: 5148

South Asian (SAS) AF: 0.179 AC: 861 AN: 4812

European-Finnish (FIN) AF: 0.112 AC: 1192 AN: 10602

Middle Eastern (MID) AF: 0.139 AC: 41 AN: 294

European-Non Finnish (NFE) AF: 0.134 AC: 9089 AN: 67986

Other (OTH) AF: 0.159 AC: 337 AN: 2116

Alfa AF: 0.150 Hom.: 244

Bravo AF: 0.170

Asia WGS AF: 0.260 AC: 905 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.72
CADD	Benign	8.2
DANN	Benign	0.92
PhyloP100		-0.35

Splicing

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

Other links and lift over

dbSNP: rs2112416; hg19: chr5-80181147;