7-86374569-C-T

Variant names:

• chr7-86374569-C-T
• rs1554888

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 0.894 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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.894 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

Gnomad4 AFR AF: 0.966

Gnomad4 AMR AF: 0.883

Gnomad4 ASJ AF: 0.846

Gnomad4 EAS AF: 0.932

Gnomad4 SAS AF: 0.886

Gnomad4 FIN AF: 0.891

Gnomad4 NFE AF: 0.855

Gnomad4 OTH AF: 0.868

Alfa AF: 0.863 Hom.: 25599

Bravo AF: 0.893

Asia WGS AF: 0.888 AC: 3090 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1554888; hg19: chr7-86003885;