rs7772564

Variant names:

• chr6-74979101-G-A
• rs7772564

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 0.032 in 152,222 control chromosomes in the GnomAD database, including 262 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 0.032 (262 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0950

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.199 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: 0.0319 AC: 4859 AN: 152104 Hom.: 260 Cov.: 32

Gnomad AFR AF: 0.0630

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0409

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.210

Gnomad SAS AF: 0.0479

Gnomad FIN AF: 0.00245

Gnomad MID AF: 0.0190

Gnomad NFE AF: 0.00323

Gnomad OTH AF: 0.0263

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

GnomAD4 genome AF: 0.0320 AC: 4870 AN: 152222 Hom.: 262 Cov.: 32 AF XY: 0.0335 AC XY: 2493 AN XY: 74428

Gnomad4 AFR AF: 0.0633

Gnomad4 AMR AF: 0.0408

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.209

Gnomad4 SAS AF: 0.0473

Gnomad4 FIN AF: 0.00245

Gnomad4 NFE AF: 0.00323

Gnomad4 OTH AF: 0.0265

Alfa AF: 0.0111 Hom.: 46

Bravo AF: 0.0361

Asia WGS AF: 0.102 AC: 352 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.2
DANN	Benign	0.54

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7772564; hg19: chr6-75688817;