chr6-148574837-C-T

Position:

• chr6-148574837-C-T

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 0.177 in 152,132 control chromosomes in the GnomAD database, including 2,448 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 0.18 (2448 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00900

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.225 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.177 AC: 26856 AN: 152012 Hom.: 2445 Cov.: 33

Gnomad AFR AF: 0.199

Gnomad AMI AF: 0.162

Gnomad AMR AF: 0.188

Gnomad ASJ AF: 0.187

Gnomad EAS AF: 0.235

Gnomad SAS AF: 0.119

Gnomad FIN AF: 0.0971

Gnomad MID AF: 0.158

Gnomad NFE AF: 0.172

Gnomad OTH AF: 0.205

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

GnomAD4 genome AF: 0.177 AC: 26885 AN: 152132 Hom.: 2448 Cov.: 33 AF XY: 0.174 AC XY: 12955 AN XY: 74366

Gnomad4 AFR AF: 0.199

Gnomad4 AMR AF: 0.188

Gnomad4 ASJ AF: 0.187

Gnomad4 EAS AF: 0.236

Gnomad4 SAS AF: 0.118

Gnomad4 FIN AF: 0.0971

Gnomad4 NFE AF: 0.172

Gnomad4 OTH AF: 0.206

Alfa AF: 0.179 Hom.: 2803

Bravo AF: 0.187

Asia WGS AF: 0.197 AC: 685 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.85
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: rs10484601; hg19: chr6-148895973;