5-121643185-C-G

Variant names:

• chr5-121643185-C-G
• rs1605727

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 0.486 in 151,840 control chromosomes in the GnomAD database, including 18,254 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 0.49 (18254 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.22
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.08).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.597 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.486 AC: 73802 AN: 151722 Hom.: 18243 Cov.: 31

Gnomad AFR AF: 0.434

Gnomad AMI AF: 0.523

Gnomad AMR AF: 0.579

Gnomad ASJ AF: 0.462

Gnomad EAS AF: 0.615

Gnomad SAS AF: 0.468

Gnomad FIN AF: 0.510

Gnomad MID AF: 0.465

Gnomad NFE AF: 0.486

Gnomad OTH AF: 0.478

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

GnomAD4 genome AF: 0.486 AC: 73861 AN: 151840 Hom.: 18254 Cov.: 31 AF XY: 0.488 AC XY: 36199 AN XY: 74190

African (AFR) AF: 0.434 AC: 17979 AN: 41400

American (AMR) AF: 0.580 AC: 8842 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.462 AC: 1604 AN: 3470

East Asian (EAS) AF: 0.615 AC: 3170 AN: 5152

South Asian (SAS) AF: 0.468 AC: 2253 AN: 4810

European-Finnish (FIN) AF: 0.510 AC: 5373 AN: 10538

Middle Eastern (MID) AF: 0.469 AC: 138 AN: 294

European-Non Finnish (NFE) AF: 0.486 AC: 33021 AN: 67908

Other (OTH) AF: 0.476 AC: 1005 AN: 2112

Alfa AF: 0.333 Hom.: 819

Bravo AF: 0.494

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.071
DANN	Benign	0.34
PhyloP100		-3.2

Splicing

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

Other links and lift over

dbSNP: rs1605727; hg19: chr5-120978880;