6-149116448-C-T

Variant names:

• chr6-149116448-C-T
• rs6900527

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 0.173 in 152,102 control chromosomes in the GnomAD database, including 2,421 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 0.17 (2421 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.75

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 (NFE) allele frequency at 95% confidence interval = 0.181 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: 0.173 AC: 26311 AN: 151984 Hom.: 2423 Cov.: 32

Gnomad AFR AF: 0.175

Gnomad AMI AF: 0.132

Gnomad AMR AF: 0.117

Gnomad ASJ AF: 0.155

Gnomad EAS AF: 0.0408

Gnomad SAS AF: 0.176

Gnomad FIN AF: 0.250

Gnomad MID AF: 0.155

Gnomad NFE AF: 0.184

Gnomad OTH AF: 0.173

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

GnomAD4 genome AF: 0.173 AC: 26327 AN: 152102 Hom.: 2421 Cov.: 32 AF XY: 0.175 AC XY: 12974 AN XY: 74342

Gnomad4 AFR AF: 0.175

Gnomad4 AMR AF: 0.117

Gnomad4 ASJ AF: 0.155

Gnomad4 EAS AF: 0.0407

Gnomad4 SAS AF: 0.176

Gnomad4 FIN AF: 0.250

Gnomad4 NFE AF: 0.184

Gnomad4 OTH AF: 0.173

Alfa AF: 0.177 Hom.: 4865

Bravo AF: 0.160

Asia WGS AF: 0.144 AC: 499 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	0.21
DANN	Benign	0.65

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6900527; hg19: chr6-149437584;