9-1553378-T-C

Variant names:

• chr9-1553378-T-C
• rs2486443

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 0.957 in 152,180 control chromosomes in the GnomAD database, including 69,789 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 0.96 (69789 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.347
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.981 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: 0.957 AC: 145563 AN: 152062 Hom.: 69734 Cov.: 30

Gnomad AFR AF: 0.989

Gnomad AMI AF: 0.945

Gnomad AMR AF: 0.964

Gnomad ASJ AF: 0.932

Gnomad EAS AF: 0.999

Gnomad SAS AF: 0.982

Gnomad FIN AF: 0.959

Gnomad MID AF: 0.987

Gnomad NFE AF: 0.932

Gnomad OTH AF: 0.965

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

GnomAD4 genome AF: 0.957 AC: 145676 AN: 152180 Hom.: 69789 Cov.: 30 AF XY: 0.959 AC XY: 71382 AN XY: 74396

African (AFR) AF: 0.989 AC: 41068 AN: 41534

American (AMR) AF: 0.964 AC: 14732 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.932 AC: 3232 AN: 3468

East Asian (EAS) AF: 0.999 AC: 5161 AN: 5164

South Asian (SAS) AF: 0.983 AC: 4722 AN: 4806

European-Finnish (FIN) AF: 0.959 AC: 10161 AN: 10596

Middle Eastern (MID) AF: 0.986 AC: 290 AN: 294

European-Non Finnish (NFE) AF: 0.932 AC: 63405 AN: 68006

Other (OTH) AF: 0.966 AC: 2043 AN: 2116

Alfa AF: 0.942 Hom.: 101670

Bravo AF: 0.960

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	1.9
DANN	Benign	0.58
PhyloP100		-0.35

Splicing

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

Other links and lift over

dbSNP: rs2486443; hg19: chr9-1553378;