8-2372045-T-C

Variant names:

• chr8-2372045-T-C
• rs897445

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 0.591 in 151,862 control chromosomes in the GnomAD database, including 26,557 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 0.59 (26557 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.312
• Publications: 7 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.587 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: 0.591 AC: 89662 AN: 151744 Hom.: 26523 Cov.: 31

Gnomad AFR AF: 0.582

Gnomad AMI AF: 0.578

Gnomad AMR AF: 0.568

Gnomad ASJ AF: 0.592

Gnomad EAS AF: 0.582

Gnomad SAS AF: 0.555

Gnomad FIN AF: 0.678

Gnomad MID AF: 0.587

Gnomad NFE AF: 0.592

Gnomad OTH AF: 0.573

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

GnomAD4 genome AF: 0.591 AC: 89745 AN: 151862 Hom.: 26557 Cov.: 31 AF XY: 0.594 AC XY: 44073 AN XY: 74226

African (AFR) AF: 0.582 AC: 24080 AN: 41374

American (AMR) AF: 0.568 AC: 8670 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.592 AC: 2054 AN: 3470

East Asian (EAS) AF: 0.582 AC: 3002 AN: 5154

South Asian (SAS) AF: 0.555 AC: 2670 AN: 4814

European-Finnish (FIN) AF: 0.678 AC: 7147 AN: 10546

Middle Eastern (MID) AF: 0.583 AC: 169 AN: 290

European-Non Finnish (NFE) AF: 0.592 AC: 40226 AN: 67934

Other (OTH) AF: 0.569 AC: 1201 AN: 2110

Alfa AF: 0.582 Hom.: 55175

Bravo AF: 0.580

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	2.1
PhyloP100		-0.31

Splicing

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

Other links and lift over

dbSNP: rs897445; hg19: chr8-2295755;