6-29950325-T-G

Variant names:

• chr6-29950325-T-G
• rs9260378

Variant summary

Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_Strong

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 0.0035 (0 hom., cov: 32)
  • Failed GnomAD Quality Control
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.89

ACMG classification

Verdict is Likely_benign. Variant got -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).

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: 0.00 AC: 497 AN: 141134 Hom.: 0 Cov.: 32 FAILED QC

Gnomad AFR AF: 0.00835

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00503

Gnomad ASJ AF: 0.00156

Gnomad EAS AF: 0.00604

Gnomad SAS AF: 0.00820

Gnomad FIN AF: 0.000287

Gnomad MID AF: 0.00352

Gnomad NFE AF: 0.000734

Gnomad OTH AF: 0.00261

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

GnomAD4 genome Data not reliable, filtered out with message: AS_VQSR AF: 0.00354 AC: 500 AN: 141228 Hom.: 0 Cov.: 32 AF XY: 0.00334 AC XY: 231 AN XY: 69240

Gnomad4 AFR AF: 0.00832

Gnomad4 AMR AF: 0.00517

Gnomad4 ASJ AF: 0.00156

Gnomad4 EAS AF: 0.00606

Gnomad4 SAS AF: 0.00844

Gnomad4 FIN AF: 0.000287

Gnomad4 NFE AF: 0.000734

Gnomad4 OTH AF: 0.00260

Alfa AF: 0.00110 Hom.: 9

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	1.6
DANN	Benign	0.26

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9260378; hg19: chr6-29918102;