rs7758790

Variant names:

• chr6-31585073-T-C
• rs7758790

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 0.224 in 151,538 control chromosomes in the GnomAD database, including 3,900 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 0.22 (3900 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.757

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.386 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: 0.224 AC: 33968 AN: 151424 Hom.: 3894 Cov.: 31

Gnomad AFR AF: 0.210

Gnomad AMI AF: 0.214

Gnomad AMR AF: 0.206

Gnomad ASJ AF: 0.272

Gnomad EAS AF: 0.173

Gnomad SAS AF: 0.402

Gnomad FIN AF: 0.182

Gnomad MID AF: 0.290

Gnomad NFE AF: 0.231

Gnomad OTH AF: 0.266

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

GnomAD4 genome AF: 0.224 AC: 34012 AN: 151538 Hom.: 3900 Cov.: 31 AF XY: 0.225 AC XY: 16633 AN XY: 74032

Gnomad4 AFR AF: 0.211

Gnomad4 AMR AF: 0.206

Gnomad4 ASJ AF: 0.272

Gnomad4 EAS AF: 0.172

Gnomad4 SAS AF: 0.401

Gnomad4 FIN AF: 0.182

Gnomad4 NFE AF: 0.231

Gnomad4 OTH AF: 0.266

Alfa AF: 0.219 Hom.: 485

Bravo AF: 0.224

Asia WGS AF: 0.290 AC: 1006 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	1.2
DANN	Benign	0.64

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7758790; hg19: chr6-31552850;