5-122746145-C-T

Variant names:

• chr5-122746145-C-T
• rs7727137

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 0.455 in 151,876 control chromosomes in the GnomAD database, including 15,865 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 0.45 (15865 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.99
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.06).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.471 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: 0.455 AC: 69021 AN: 151758 Hom.: 15848 Cov.: 32

Gnomad AFR AF: 0.476

Gnomad AMI AF: 0.553

Gnomad AMR AF: 0.480

Gnomad ASJ AF: 0.430

Gnomad EAS AF: 0.417

Gnomad SAS AF: 0.300

Gnomad FIN AF: 0.541

Gnomad MID AF: 0.408

Gnomad NFE AF: 0.437

Gnomad OTH AF: 0.466

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

GnomAD4 genome AF: 0.455 AC: 69068 AN: 151876 Hom.: 15865 Cov.: 32 AF XY: 0.455 AC XY: 33803 AN XY: 74226

African (AFR) AF: 0.475 AC: 19657 AN: 41358

American (AMR) AF: 0.480 AC: 7333 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.430 AC: 1489 AN: 3466

East Asian (EAS) AF: 0.415 AC: 2143 AN: 5158

South Asian (SAS) AF: 0.300 AC: 1444 AN: 4810

European-Finnish (FIN) AF: 0.541 AC: 5709 AN: 10548

Middle Eastern (MID) AF: 0.408 AC: 120 AN: 294

European-Non Finnish (NFE) AF: 0.437 AC: 29677 AN: 67942

Other (OTH) AF: 0.470 AC: 993 AN: 2112

Alfa AF: 0.455 Hom.: 4502

Bravo AF: 0.455

Asia WGS AF: 0.379 AC: 1317 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.0040
DANN	Benign	0.37
PhyloP100		-2.0

Splicing

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

Other links and lift over

dbSNP: rs7727137; hg19: chr5-122081840;