7-86374569-C-T

Variant names:

• chr7-86374569-C-T
• rs1554888

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 0.894 in 152,158 control chromosomes in the GnomAD database, including 61,010 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 0.89 (61010 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.313
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.958 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.894 AC: 135873 AN: 152040 Hom.: 60946 Cov.: 31

Gnomad AFR AF: 0.966

Gnomad AMI AF: 0.776

Gnomad AMR AF: 0.882

Gnomad ASJ AF: 0.846

Gnomad EAS AF: 0.932

Gnomad SAS AF: 0.886

Gnomad FIN AF: 0.891

Gnomad MID AF: 0.807

Gnomad NFE AF: 0.855

Gnomad OTH AF: 0.868

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

GnomAD4 genome AF: 0.894 AC: 135994 AN: 152158 Hom.: 61010 Cov.: 31 AF XY: 0.895 AC XY: 66554 AN XY: 74382

African (AFR) AF: 0.966 AC: 40135 AN: 41536

American (AMR) AF: 0.883 AC: 13479 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.846 AC: 2933 AN: 3468

East Asian (EAS) AF: 0.932 AC: 4821 AN: 5172

South Asian (SAS) AF: 0.886 AC: 4273 AN: 4824

European-Finnish (FIN) AF: 0.891 AC: 9428 AN: 10586

Middle Eastern (MID) AF: 0.810 AC: 238 AN: 294

European-Non Finnish (NFE) AF: 0.855 AC: 58154 AN: 67994

Other (OTH) AF: 0.868 AC: 1825 AN: 2102

Alfa AF: 0.862 Hom.: 28420

Bravo AF: 0.893

Asia WGS AF: 0.888 AC: 3090 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	5.7
DANN	Benign	0.74
PhyloP100		0.31

Splicing

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

Other links and lift over

dbSNP: rs1554888; hg19: chr7-86003885;