rs112730887

Variant names:

• chr5-62945099-T-C
• rs112730887

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 0.044 in 152,096 control chromosomes in the GnomAD database, including 329 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 0.044 (329 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.98
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.111 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: 0.0438 AC: 6654 AN: 151978 Hom.: 324 Cov.: 32

Gnomad AFR AF: 0.114

Gnomad AMI AF: 0.00439

Gnomad AMR AF: 0.0263

Gnomad ASJ AF: 0.00865

Gnomad EAS AF: 0.102

Gnomad SAS AF: 0.0738

Gnomad FIN AF: 0.00151

Gnomad MID AF: 0.0253

Gnomad NFE AF: 0.00788

Gnomad OTH AF: 0.0402

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

GnomAD4 genome AF: 0.0440 AC: 6685 AN: 152096 Hom.: 329 Cov.: 32 AF XY: 0.0436 AC XY: 3239 AN XY: 74366

African (AFR) AF: 0.114 AC: 4719 AN: 41460

American (AMR) AF: 0.0263 AC: 402 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.00865 AC: 30 AN: 3468

East Asian (EAS) AF: 0.102 AC: 525 AN: 5150

South Asian (SAS) AF: 0.0743 AC: 358 AN: 4820

European-Finnish (FIN) AF: 0.00151 AC: 16 AN: 10604

Middle Eastern (MID) AF: 0.0238 AC: 7 AN: 294

European-Non Finnish (NFE) AF: 0.00790 AC: 537 AN: 67998

Other (OTH) AF: 0.0412 AC: 87 AN: 2110

Alfa AF: 0.0324 Hom.: 24

Bravo AF: 0.0478

Asia WGS AF: 0.0880 AC: 305 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	0.21
DANN	Benign	0.61
PhyloP100		-3.0

Splicing

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

Other links and lift over

dbSNP: rs112730887; hg19: chr5-62240926;