6-29964515-G-T

Variant names:

• chr6-29964515-G-T
• rs2523933

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 0.269 in 151,970 control chromosomes in the GnomAD database, including 5,776 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 0.27 (5776 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.01

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.62).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.293 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: 0.270 AC: 40935 AN: 151856 Hom.: 5767 Cov.: 32

Gnomad AFR AF: 0.214

Gnomad AMI AF: 0.425

Gnomad AMR AF: 0.250

Gnomad ASJ AF: 0.258

Gnomad EAS AF: 0.245

Gnomad SAS AF: 0.302

Gnomad FIN AF: 0.328

Gnomad MID AF: 0.282

Gnomad NFE AF: 0.297

Gnomad OTH AF: 0.258

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

GnomAD4 genome AF: 0.269 AC: 40945 AN: 151970 Hom.: 5776 Cov.: 32 AF XY: 0.270 AC XY: 20085 AN XY: 74310

Gnomad4 AFR AF: 0.214

Gnomad4 AMR AF: 0.250

Gnomad4 ASJ AF: 0.258

Gnomad4 EAS AF: 0.245

Gnomad4 SAS AF: 0.300

Gnomad4 FIN AF: 0.328

Gnomad4 NFE AF: 0.297

Gnomad4 OTH AF: 0.265

Alfa AF: 0.212 Hom.: 887

Bravo AF: 0.259

Asia WGS AF: 0.343 AC: 1184 AN: 3452

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.62
CADD	Benign	11
DANN	Benign	0.93

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2523933; hg19: chr6-29932292;