rs7775759

Variant names:

• chr6-31384669-G-A
• rs7775759

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 0.361 in 152,102 control chromosomes in the GnomAD database, including 10,252 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 0.36 (10252 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.221

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.416 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: 0.361 AC: 54805 AN: 151984 Hom.: 10239 Cov.: 32

Gnomad AFR AF: 0.381

Gnomad AMI AF: 0.509

Gnomad AMR AF: 0.424

Gnomad ASJ AF: 0.604

Gnomad EAS AF: 0.317

Gnomad SAS AF: 0.416

Gnomad FIN AF: 0.401

Gnomad MID AF: 0.446

Gnomad NFE AF: 0.311

Gnomad OTH AF: 0.393

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

GnomAD4 genome AF: 0.361 AC: 54861 AN: 152102 Hom.: 10252 Cov.: 32 AF XY: 0.366 AC XY: 27245 AN XY: 74346

Gnomad4 AFR AF: 0.381

Gnomad4 AMR AF: 0.424

Gnomad4 ASJ AF: 0.604

Gnomad4 EAS AF: 0.318

Gnomad4 SAS AF: 0.416

Gnomad4 FIN AF: 0.401

Gnomad4 NFE AF: 0.311

Gnomad4 OTH AF: 0.396

Alfa AF: 0.342 Hom.: 3539

Bravo AF: 0.363

Asia WGS AF: 0.350 AC: 1218 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	7.6
DANN	Benign	0.65

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7775759; hg19: chr6-31352446;