chr5-112696878-G-T

Variant names:

• chr5-112696878-G-T
• rs60905866

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 0.059 in 152,188 control chromosomes in the GnomAD database, including 532 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 0.059 (532 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.347
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.137 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: 0.0590 AC: 8970 AN: 152070 Hom.: 529 Cov.: 32

Gnomad AFR AF: 0.140

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0304

Gnomad ASJ AF: 0.0320

Gnomad EAS AF: 0.134

Gnomad SAS AF: 0.0713

Gnomad FIN AF: 0.00604

Gnomad MID AF: 0.0348

Gnomad NFE AF: 0.0194

Gnomad OTH AF: 0.0727

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

GnomAD4 genome AF: 0.0590 AC: 8982 AN: 152188 Hom.: 532 Cov.: 32 AF XY: 0.0595 AC XY: 4423 AN XY: 74386

African (AFR) AF: 0.140 AC: 5822 AN: 41496

American (AMR) AF: 0.0303 AC: 464 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.0320 AC: 111 AN: 3470

East Asian (EAS) AF: 0.134 AC: 694 AN: 5182

South Asian (SAS) AF: 0.0710 AC: 342 AN: 4818

European-Finnish (FIN) AF: 0.00604 AC: 64 AN: 10598

Middle Eastern (MID) AF: 0.0340 AC: 10 AN: 294

European-Non Finnish (NFE) AF: 0.0195 AC: 1323 AN: 68016

Other (OTH) AF: 0.0720 AC: 152 AN: 2112

Alfa AF: 0.0346 Hom.: 404

Bravo AF: 0.0651

Asia WGS AF: 0.114 AC: 396 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	4.3
DANN	Benign	0.64
PhyloP100		0.35

Splicing

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

Other links and lift over

dbSNP: rs60905866; hg19: chr5-112032575;