chr6-29790748-T-C

Position:

• chr6-29790748-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 0.405 in 152,150 control chromosomes in the GnomAD database, including 13,506 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 0.41 (13506 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0330

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.562 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.405 AC: 61571 AN: 152032 Hom.: 13484 Cov.: 33

Gnomad AFR AF: 0.568

Gnomad AMI AF: 0.205

Gnomad AMR AF: 0.415

Gnomad ASJ AF: 0.495

Gnomad EAS AF: 0.202

Gnomad SAS AF: 0.355

Gnomad FIN AF: 0.207

Gnomad MID AF: 0.528

Gnomad NFE AF: 0.350

Gnomad OTH AF: 0.430

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

GnomAD4 genome AF: 0.405 AC: 61631 AN: 152150 Hom.: 13506 Cov.: 33 AF XY: 0.396 AC XY: 29452 AN XY: 74376

Gnomad4 AFR AF: 0.568

Gnomad4 AMR AF: 0.415

Gnomad4 ASJ AF: 0.495

Gnomad4 EAS AF: 0.202

Gnomad4 SAS AF: 0.356

Gnomad4 FIN AF: 0.207

Gnomad4 NFE AF: 0.350

Gnomad4 OTH AF: 0.424

Alfa AF: 0.408 Hom.: 1199

Bravo AF: 0.431

Asia WGS AF: 0.288 AC: 1004 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	5.7
DANN	Benign	0.59

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1610640; hg19: chr6-29758525;