rs7772564

Variant names:

• chr6-74979101-G-A
• rs7772564

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.0633 AC: 2629 AN: 41526

American (AMR) AF: 0.0408 AC: 624 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 3466

East Asian (EAS) AF: 0.209 AC: 1081 AN: 5162

South Asian (SAS) AF: 0.0473 AC: 228 AN: 4822

European-Finnish (FIN) AF: 0.00245 AC: 26 AN: 10616

Middle Eastern (MID) AF: 0.0204 AC: 6 AN: 294

European-Non Finnish (NFE) AF: 0.00323 AC: 220 AN: 68022

Other (OTH) AF: 0.0265 AC: 56 AN: 2114

Alfa AF: 0.0156 Hom.: 116

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
PhyloP100		0.095

Splicing

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

Other links and lift over

dbSNP: rs7772564; hg19: chr6-75688817;