rs7772056

Variant names:

• chr6-19879337-C-T
• rs7772056

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 0.43 in 152,036 control chromosomes in the GnomAD database, including 14,447 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 0.43 (14447 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0980

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.503 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: 0.430 AC: 65283 AN: 151922 Hom.: 14412 Cov.: 32

Gnomad AFR AF: 0.508

Gnomad AMI AF: 0.245

Gnomad AMR AF: 0.484

Gnomad ASJ AF: 0.383

Gnomad EAS AF: 0.427

Gnomad SAS AF: 0.350

Gnomad FIN AF: 0.484

Gnomad MID AF: 0.392

Gnomad NFE AF: 0.373

Gnomad OTH AF: 0.407

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

GnomAD4 genome AF: 0.430 AC: 65365 AN: 152036 Hom.: 14447 Cov.: 32 AF XY: 0.434 AC XY: 32228 AN XY: 74322

Gnomad4 AFR AF: 0.509

Gnomad4 AMR AF: 0.484

Gnomad4 ASJ AF: 0.383

Gnomad4 EAS AF: 0.428

Gnomad4 SAS AF: 0.349

Gnomad4 FIN AF: 0.484

Gnomad4 NFE AF: 0.373

Gnomad4 OTH AF: 0.406

Alfa AF: 0.388 Hom.: 14971

Bravo AF: 0.438

Asia WGS AF: 0.442 AC: 1532 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.29
DANN	Benign	0.39

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7772056; hg19: chr6-19879568;