6-29008294-T-C

Variant names:

• chr6-29008294-T-C
• rs6923005

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.343 in 152,074 control chromosomes in the GnomAD database, including 10,413 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 0.34 (10413 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.165
• Publications: 12 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.544 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: 0.343 AC: 52172 AN: 151956 Hom.: 10392 Cov.: 32

Gnomad AFR AF: 0.550

Gnomad AMI AF: 0.209

Gnomad AMR AF: 0.294

Gnomad ASJ AF: 0.381

Gnomad EAS AF: 0.226

Gnomad SAS AF: 0.355

Gnomad FIN AF: 0.290

Gnomad MID AF: 0.266

Gnomad NFE AF: 0.246

Gnomad OTH AF: 0.341

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

GnomAD4 genome AF: 0.343 AC: 52233 AN: 152074 Hom.: 10413 Cov.: 32 AF XY: 0.346 AC XY: 25688 AN XY: 74324

African (AFR) AF: 0.550 AC: 22811 AN: 41454

American (AMR) AF: 0.293 AC: 4485 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.381 AC: 1323 AN: 3470

East Asian (EAS) AF: 0.225 AC: 1166 AN: 5178

South Asian (SAS) AF: 0.354 AC: 1707 AN: 4820

European-Finnish (FIN) AF: 0.290 AC: 3063 AN: 10562

Middle Eastern (MID) AF: 0.255 AC: 75 AN: 294

European-Non Finnish (NFE) AF: 0.246 AC: 16700 AN: 67982

Other (OTH) AF: 0.338 AC: 713 AN: 2112

Alfa AF: 0.279 Hom.: 6863

Bravo AF: 0.356

Asia WGS AF: 0.278 AC: 971 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	9.8
DANN	Benign	0.72
PhyloP100		0.17

Splicing

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

Other links and lift over

dbSNP: rs6923005; hg19: chr6-28976071;