5-112698656-A-T

Variant names:

• chr5-112698656-A-T
• rs2900066

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 0.58 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
• Publications: 4 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.599 AC: 24828 AN: 41460

American (AMR) AF: 0.645 AC: 9850 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.529 AC: 1837 AN: 3472

East Asian (EAS) AF: 0.812 AC: 4215 AN: 5190

South Asian (SAS) AF: 0.641 AC: 3091 AN: 4822

European-Finnish (FIN) AF: 0.491 AC: 5181 AN: 10560

Middle Eastern (MID) AF: 0.527 AC: 155 AN: 294

European-Non Finnish (NFE) AF: 0.549 AC: 37310 AN: 67982

Other (OTH) AF: 0.588 AC: 1240 AN: 2108

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
PhyloP100		-0.40

Splicing

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

Other links and lift over

dbSNP: rs2900066; hg19: chr5-112034353;