rs7753826

Positions:

• chr6-26042011-T-A
• chr6-26042011-T-C
• chr6-26042011-T-G

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 0.203 in 151,974 control chromosomes in the GnomAD database, including 3,694 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 0.20 (3694 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.01

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.535 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.203 AC: 30885 AN: 151856 Hom.: 3693 Cov.: 31

Gnomad AFR AF: 0.145

Gnomad AMI AF: 0.114

Gnomad AMR AF: 0.280

Gnomad ASJ AF: 0.194

Gnomad EAS AF: 0.553

Gnomad SAS AF: 0.300

Gnomad FIN AF: 0.172

Gnomad MID AF: 0.212

Gnomad NFE AF: 0.194

Gnomad OTH AF: 0.238

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

GnomAD4 genome AF: 0.203 AC: 30897 AN: 151974 Hom.: 3694 Cov.: 31 AF XY: 0.209 AC XY: 15523 AN XY: 74292

Gnomad4 AFR AF: 0.145

Gnomad4 AMR AF: 0.281

Gnomad4 ASJ AF: 0.194

Gnomad4 EAS AF: 0.552

Gnomad4 SAS AF: 0.299

Gnomad4 FIN AF: 0.172

Gnomad4 NFE AF: 0.194

Gnomad4 OTH AF: 0.238

Alfa AF: 0.106 Hom.: 154

Bravo AF: 0.209

Asia WGS AF: 0.382 AC: 1326 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	3.1
DANN	Benign	0.48

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7753826; hg19: chr6-26042239;