chr5-57138557-T-C

Variant names:

• chr5-57138557-T-C
• rs186682

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BP4_Strong BS2

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 0.023 (11 hom., cov: 0)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.351
• Publications: 0 publications found

ACMG classification

Our verdict: Benign. The variant received -8 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BS2: High Homozygotes in GnomAd4 at 11 gene

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.0230 AC: 758 AN: 32986 Hom.: 11 Cov.: 0

Gnomad AFR AF: 0.0302

Gnomad AMI AF: 0.00446

Gnomad AMR AF: 0.0213

Gnomad ASJ AF: 0.0313

Gnomad EAS AF: 0.00931

Gnomad SAS AF: 0.0371

Gnomad FIN AF: 0.0329

Gnomad MID AF: 0.0536

Gnomad NFE AF: 0.0192

Gnomad OTH AF: 0.0332

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

GnomAD4 genome AF: 0.0230 AC: 758 AN: 33028 Hom.: 11 Cov.: 0 AF XY: 0.0240 AC XY: 379 AN XY: 15788

⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5.

African (AFR) AF: 0.0301 AC: 279 AN: 9266

American (AMR) AF: 0.0213 AC: 74 AN: 3474

Ashkenazi Jewish (ASJ) AF: 0.0313 AC: 22 AN: 704

East Asian (EAS) AF: 0.00934 AC: 28 AN: 2998

South Asian (SAS) AF: 0.0369 AC: 35 AN: 948

European-Finnish (FIN) AF: 0.0329 AC: 38 AN: 1154

Middle Eastern (MID) AF: 0.0625 AC: 3 AN: 48

European-Non Finnish (NFE) AF: 0.0192 AC: 264 AN: 13772

Other (OTH) AF: 0.0318 AC: 14 AN: 440

⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5. (p-value = 0), which strongly suggests a high chance of mosaicism in these individuals.

Alfa AF: 0.291 Hom.: 0

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.57
DANN	Benign	0.23
PhyloP100		0.35

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs186682;

hg19: chr5-56434384;

COSMIC: COSV51295569;