rs969992

chr4-45115817-T-C

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 0.398 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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	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

Gnomad4 AFR AF: 0.327

Gnomad4 AMR AF: 0.505

Gnomad4 ASJ AF: 0.460

Gnomad4 EAS AF: 0.481

Gnomad4 SAS AF: 0.574

Gnomad4 FIN AF: 0.364

Gnomad4 NFE AF: 0.400

Gnomad4 OTH AF: 0.425

Alfa AF: 0.398 Hom.: 1535

Bravo AF: 0.403

Asia WGS AF: 0.528 AC: 1834 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
Cadd	Benign	1.3
Dann	Benign	0.53

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs969992; hg19: chr4-45117834;