6-29540496-T-C

Position:

• chr6-29540496-T-C

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 0.0848 in 152,252 control chromosomes in the GnomAD database, including 1,563 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 0.085 (1563 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.283

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 (AFR) allele frequency at 95% confidence interval = 0.263 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: 0.0846 AC: 12864 AN: 152134 Hom.: 1556 Cov.: 32

Gnomad AFR AF: 0.267

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0512

Gnomad ASJ AF: 0.0190

Gnomad EAS AF: 0.0136

Gnomad SAS AF: 0.00807

Gnomad FIN AF: 0.00216

Gnomad MID AF: 0.0158

Gnomad NFE AF: 0.00975

Gnomad OTH AF: 0.0768

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

GnomAD4 genome AF: 0.0848 AC: 12905 AN: 152252 Hom.: 1563 Cov.: 32 AF XY: 0.0822 AC XY: 6119 AN XY: 74462

Gnomad4 AFR AF: 0.267

Gnomad4 AMR AF: 0.0510

Gnomad4 ASJ AF: 0.0190

Gnomad4 EAS AF: 0.0137

Gnomad4 SAS AF: 0.00787

Gnomad4 FIN AF: 0.00216

Gnomad4 NFE AF: 0.00975

Gnomad4 OTH AF: 0.0755

Alfa AF: 0.0183 Hom.: 207

Bravo AF: 0.0980

Asia WGS AF: 0.0220 AC: 78 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	5.4
DANN	Benign	0.64

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10484548; hg19: chr6-29508273;