chr6-24648227-T-C

Variant names:

• chr6-24648227-T-C
• rs3212236

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.225 in 152,162 control chromosomes in the GnomAD database, including 4,842 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 0.23 (4842 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.598

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.614 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: 0.225 AC: 34233 AN: 152044 Hom.: 4841 Cov.: 31

Gnomad AFR AF: 0.205

Gnomad AMI AF: 0.358

Gnomad AMR AF: 0.367

Gnomad ASJ AF: 0.210

Gnomad EAS AF: 0.632

Gnomad SAS AF: 0.431

Gnomad FIN AF: 0.124

Gnomad MID AF: 0.323

Gnomad NFE AF: 0.174

Gnomad OTH AF: 0.241

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

GnomAD4 genome AF: 0.225 AC: 34252 AN: 152162 Hom.: 4842 Cov.: 31 AF XY: 0.230 AC XY: 17134 AN XY: 74410

Gnomad4 AFR AF: 0.205

Gnomad4 AMR AF: 0.367

Gnomad4 ASJ AF: 0.210

Gnomad4 EAS AF: 0.632

Gnomad4 SAS AF: 0.429

Gnomad4 FIN AF: 0.124

Gnomad4 NFE AF: 0.174

Gnomad4 OTH AF: 0.243

Alfa AF: 0.184 Hom.: 966

Bravo AF: 0.240

Asia WGS AF: 0.504 AC: 1751 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.84
DANN	Benign	0.74

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3212236; hg19: chr6-24648455;