chr7-12246599-G-A

Variant names:

• chr7-12246599-G-A
• rs1548882

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 0.605 in 151,154 control chromosomes in the GnomAD database, including 28,409 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 0.60 (28409 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.324
• Publications: 4 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.754 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.604 AC: 91303 AN: 151040 Hom.: 28378 Cov.: 31

Gnomad AFR AF: 0.760

Gnomad AMI AF: 0.441

Gnomad AMR AF: 0.599

Gnomad ASJ AF: 0.546

Gnomad EAS AF: 0.606

Gnomad SAS AF: 0.634

Gnomad FIN AF: 0.535

Gnomad MID AF: 0.609

Gnomad NFE AF: 0.525

Gnomad OTH AF: 0.580

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

GnomAD4 genome AF: 0.605 AC: 91392 AN: 151154 Hom.: 28409 Cov.: 31 AF XY: 0.607 AC XY: 44835 AN XY: 73842

African (AFR) AF: 0.761 AC: 31452 AN: 41348

American (AMR) AF: 0.599 AC: 9070 AN: 15148

Ashkenazi Jewish (ASJ) AF: 0.546 AC: 1895 AN: 3470

East Asian (EAS) AF: 0.608 AC: 3127 AN: 5144

South Asian (SAS) AF: 0.632 AC: 3043 AN: 4812

European-Finnish (FIN) AF: 0.535 AC: 5437 AN: 10162

Middle Eastern (MID) AF: 0.610 AC: 177 AN: 290

European-Non Finnish (NFE) AF: 0.525 AC: 35578 AN: 67772

Other (OTH) AF: 0.578 AC: 1213 AN: 2100

Alfa AF: 0.545 Hom.: 5600

Bravo AF: 0.616

Asia WGS AF: 0.604 AC: 2080 AN: 3448

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	2.0
DANN	Benign	0.56
PhyloP100		0.32

Splicing

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

Other links and lift over

dbSNP: rs1548882; hg19: chr7-12286225; COSMIC: COSV67543892;