rs6934903

Positions:

• chr6-135130426-T-A
• chr6-135130426-T-C

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_Strong BP6 BA1

The variant allele was found at a frequency of 0.146 in 152,154 control chromosomes in the GnomAD database, including 2,031 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in Lovd as Likely benign (no stars).

• Frequency: Genomes: 𝑓 0.15 (2031 hom., cov: 31)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.258

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -13 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BP6: Variant 6-135130426-T-A is Benign according to our data. Variant chr6-135130426-T-A is described in Lovd as [Likely_benign].
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.245 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.135130426T>A		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.146 AC: 22230 AN: 152036 Hom.: 2033 Cov.: 31

Gnomad AFR AF: 0.0435

Gnomad AMI AF: 0.0735

Gnomad AMR AF: 0.145

Gnomad ASJ AF: 0.183

Gnomad EAS AF: 0.257

Gnomad SAS AF: 0.132

Gnomad FIN AF: 0.247

Gnomad MID AF: 0.152

Gnomad NFE AF: 0.186

Gnomad OTH AF: 0.132

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

GnomAD4 genome AF: 0.146 AC: 22228 AN: 152154 Hom.: 2031 Cov.: 31 AF XY: 0.148 AC XY: 10992 AN XY: 74370

Gnomad4 AFR AF: 0.0436

Gnomad4 AMR AF: 0.145

Gnomad4 ASJ AF: 0.183

Gnomad4 EAS AF: 0.257

Gnomad4 SAS AF: 0.132

Gnomad4 FIN AF: 0.247

Gnomad4 NFE AF: 0.186

Gnomad4 OTH AF: 0.130

Alfa AF: 0.169 Hom.: 320

Bravo AF: 0.136

Asia WGS AF: 0.171 AC: 593 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	1.6
DANN	Benign	0.50

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6934903; hg19: chr6-135451564; COSMIC: COSV58836606;