6-29817999-C-T

Variant names:

• chr6-29817999-C-T
• rs1736951

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 0.342 in 152,040 control chromosomes in the GnomAD database, including 9,141 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 (9141 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.586

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.06).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.368 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: 0.342 AC: 51975 AN: 151920 Hom.: 9128 Cov.: 31

Gnomad AFR AF: 0.373

Gnomad AMI AF: 0.261

Gnomad AMR AF: 0.375

Gnomad ASJ AF: 0.478

Gnomad EAS AF: 0.121

Gnomad SAS AF: 0.324

Gnomad FIN AF: 0.223

Gnomad MID AF: 0.468

Gnomad NFE AF: 0.346

Gnomad OTH AF: 0.362

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

GnomAD4 genome AF: 0.342 AC: 52026 AN: 152040 Hom.: 9141 Cov.: 31 AF XY: 0.335 AC XY: 24869 AN XY: 74322

Gnomad4 AFR AF: 0.373

Gnomad4 AMR AF: 0.375

Gnomad4 ASJ AF: 0.478

Gnomad4 EAS AF: 0.121

Gnomad4 SAS AF: 0.325

Gnomad4 FIN AF: 0.223

Gnomad4 NFE AF: 0.346

Gnomad4 OTH AF: 0.358

Alfa AF: 0.345 Hom.: 9082

Bravo AF: 0.357

Asia WGS AF: 0.215 AC: 751 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	1.3
DANN	Benign	0.34

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1736951; hg19: chr6-29785776;