chr4-45115817-T-C

Variant names:

• chr4-45115817-T-C
• rs969992

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 0.398 in 151,490 control chromosomes in the GnomAD database, including 12,292 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 0.40 (12292 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.175
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.557 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.398 AC: 60315 AN: 151372 Hom.: 12286 Cov.: 32

Gnomad AFR AF: 0.327

Gnomad AMI AF: 0.432

Gnomad AMR AF: 0.504

Gnomad ASJ AF: 0.460

Gnomad EAS AF: 0.481

Gnomad SAS AF: 0.574

Gnomad FIN AF: 0.364

Gnomad MID AF: 0.440

Gnomad NFE AF: 0.400

Gnomad OTH AF: 0.419

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

GnomAD4 genome AF: 0.398 AC: 60351 AN: 151490 Hom.: 12292 Cov.: 32 AF XY: 0.406 AC XY: 30069 AN XY: 74032

African (AFR) AF: 0.327 AC: 13543 AN: 41410

American (AMR) AF: 0.505 AC: 7663 AN: 15184

Ashkenazi Jewish (ASJ) AF: 0.460 AC: 1591 AN: 3462

East Asian (EAS) AF: 0.481 AC: 2477 AN: 5150

South Asian (SAS) AF: 0.574 AC: 2771 AN: 4824

European-Finnish (FIN) AF: 0.364 AC: 3849 AN: 10564

Middle Eastern (MID) AF: 0.432 AC: 127 AN: 294

European-Non Finnish (NFE) AF: 0.400 AC: 27043 AN: 67588

Other (OTH) AF: 0.425 AC: 894 AN: 2104

Alfa AF: 0.395 Hom.: 1571

Bravo AF: 0.403

Asia WGS AF: 0.528 AC: 1834 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	1.3
DANN	Benign	0.53
PhyloP100		-0.17

Splicing

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

Other links and lift over

dbSNP: rs969992; hg19: chr4-45117834;