7-53146978-A-G

Variant names:

• chr7-53146978-A-G
• rs1357963

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 0.842 in 144,586 control chromosomes in the GnomAD database, including 51,891 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 0.84 (51891 hom., cov: 25)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.72
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.941 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.842 AC: 121713 AN: 144532 Hom.: 51863 Cov.: 25

Gnomad AFR AF: 0.949

Gnomad AMI AF: 0.824

Gnomad AMR AF: 0.851

Gnomad ASJ AF: 0.856

Gnomad EAS AF: 0.957

Gnomad SAS AF: 0.846

Gnomad FIN AF: 0.736

Gnomad MID AF: 0.889

Gnomad NFE AF: 0.785

Gnomad OTH AF: 0.849

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

GnomAD4 genome AF: 0.842 AC: 121769 AN: 144586 Hom.: 51891 Cov.: 25 AF XY: 0.843 AC XY: 59158 AN XY: 70182

African (AFR) AF: 0.949 AC: 35927 AN: 37862

American (AMR) AF: 0.852 AC: 12370 AN: 14526

Ashkenazi Jewish (ASJ) AF: 0.856 AC: 2921 AN: 3414

East Asian (EAS) AF: 0.957 AC: 4670 AN: 4880

South Asian (SAS) AF: 0.845 AC: 3848 AN: 4552

European-Finnish (FIN) AF: 0.736 AC: 6926 AN: 9412

Middle Eastern (MID) AF: 0.902 AC: 249 AN: 276

European-Non Finnish (NFE) AF: 0.785 AC: 52407 AN: 66754

Other (OTH) AF: 0.850 AC: 1724 AN: 2028

Alfa AF: 0.819 Hom.: 5383

Asia WGS AF: 0.898 AC: 3018 AN: 3364

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.85
DANN	Benign	0.58
PhyloP100		-2.7

Splicing

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

Other links and lift over

dbSNP: rs1357963; hg19: chr7-53214671;