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).

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: 0.102 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 v4.3

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;