5-112698656-A-T

Variant names:

• chr5-112698656-A-T
• rs2900066

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 0.58 in 152,070 control chromosomes in the GnomAD database, including 26,007 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 0.58 (26007 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.403

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.792 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: 0.580 AC: 88116 AN: 151952 Hom.: 25982 Cov.: 32

Gnomad AFR AF: 0.598

Gnomad AMI AF: 0.539

Gnomad AMR AF: 0.645

Gnomad ASJ AF: 0.529

Gnomad EAS AF: 0.813

Gnomad SAS AF: 0.641

Gnomad FIN AF: 0.491

Gnomad MID AF: 0.528

Gnomad NFE AF: 0.549

Gnomad OTH AF: 0.590

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

GnomAD4 genome AF: 0.580 AC: 88196 AN: 152070 Hom.: 26007 Cov.: 32 AF XY: 0.582 AC XY: 43244 AN XY: 74342

Gnomad4 AFR AF: 0.599

Gnomad4 AMR AF: 0.645

Gnomad4 ASJ AF: 0.529

Gnomad4 EAS AF: 0.812

Gnomad4 SAS AF: 0.641

Gnomad4 FIN AF: 0.491

Gnomad4 NFE AF: 0.549

Gnomad4 OTH AF: 0.588

Alfa AF: 0.417 Hom.: 1113

Bravo AF: 0.596

Asia WGS AF: 0.722 AC: 2510 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.0
DANN	Benign	0.68

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2900066; hg19: chr5-112034353;