rs6933404

Positions:

• chr6-137638098-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 0.159 in 152,220 control chromosomes in the GnomAD database, including 2,122 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 0.16 (2122 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.769

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.206 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: 0.159 AC: 24169 AN: 152102 Hom.: 2121 Cov.: 32

Gnomad AFR AF: 0.110

Gnomad AMI AF: 0.159

Gnomad AMR AF: 0.124

Gnomad ASJ AF: 0.150

Gnomad EAS AF: 0.00192

Gnomad SAS AF: 0.120

Gnomad FIN AF: 0.178

Gnomad MID AF: 0.139

Gnomad NFE AF: 0.209

Gnomad OTH AF: 0.161

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

GnomAD4 genome AF: 0.159 AC: 24173 AN: 152220 Hom.: 2122 Cov.: 32 AF XY: 0.154 AC XY: 11488 AN XY: 74438

Gnomad4 AFR AF: 0.109

Gnomad4 AMR AF: 0.124

Gnomad4 ASJ AF: 0.150

Gnomad4 EAS AF: 0.00193

Gnomad4 SAS AF: 0.121

Gnomad4 FIN AF: 0.178

Gnomad4 NFE AF: 0.209

Gnomad4 OTH AF: 0.159

Alfa AF: 0.194 Hom.: 3869

Bravo AF: 0.153

Asia WGS AF: 0.0610 AC: 213 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	0.54
DANN	Benign	0.84

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6933404; hg19: chr6-137959235;