6-24648973-G-C

Variant names:

• chr6-24648973-G-C
• rs28501680

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BP4_Strong

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 0.10 (1097 hom., cov: 20)
  • Failed GnomAD Quality Control
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.335
• Publications: 2 publications found

ACMG classification

Our verdict: Likely_benign. The variant received -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).

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: 0.102 AC: 11618 AN: 113796 Hom.: 1098 Cov.: 20

Gnomad AFR AF: 0.0854

Gnomad AMI AF: 0.199

Gnomad AMR AF: 0.177

Gnomad ASJ AF: 0.106

Gnomad EAS AF: 0.456

Gnomad SAS AF: 0.228

Gnomad FIN AF: 0.0498

Gnomad MID AF: 0.198

Gnomad NFE AF: 0.0839

Gnomad OTH AF: 0.105

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

GnomAD4 genome Data not reliable, filtered out with message: AS_VQSR AF: 0.102 AC: 11627 AN: 113898 Hom.: 1097 Cov.: 20 AF XY: 0.102 AC XY: 5582 AN XY: 54940

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

African (AFR) AF: 0.0853 AC: 2572 AN: 30146

American (AMR) AF: 0.178 AC: 1614 AN: 9080

Ashkenazi Jewish (ASJ) AF: 0.106 AC: 290 AN: 2736

East Asian (EAS) AF: 0.456 AC: 1090 AN: 2388

South Asian (SAS) AF: 0.226 AC: 632 AN: 2792

European-Finnish (FIN) AF: 0.0498 AC: 441 AN: 8856

Middle Eastern (MID) AF: 0.216 AC: 42 AN: 194

European-Non Finnish (NFE) AF: 0.0839 AC: 4660 AN: 55554

Other (OTH) AF: 0.105 AC: 160 AN: 1518

⚠️ 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: 0.150 Hom.: 42

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	2.3
DANN	Benign	0.23
PhyloP100		0.34

Splicing

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

Other links and lift over

dbSNP: rs28501680; hg19: chr6-24649201;