chr4-73864663-A-C

Variant names:

• chr4-73864663-A-C
• rs2367291

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 0.454 in 152,028 control chromosomes in the GnomAD database, including 18,863 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 0.45 (18863 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.10

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.76 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: 0.454 AC: 68939 AN: 151908 Hom.: 18808 Cov.: 32

Gnomad AFR AF: 0.767

Gnomad AMI AF: 0.307

Gnomad AMR AF: 0.488

Gnomad ASJ AF: 0.389

Gnomad EAS AF: 0.408

Gnomad SAS AF: 0.377

Gnomad FIN AF: 0.310

Gnomad MID AF: 0.424

Gnomad NFE AF: 0.292

Gnomad OTH AF: 0.459

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

GnomAD4 genome AF: 0.454 AC: 69054 AN: 152028 Hom.: 18863 Cov.: 32 AF XY: 0.454 AC XY: 33700 AN XY: 74306

Gnomad4 AFR AF: 0.767

Gnomad4 AMR AF: 0.488

Gnomad4 ASJ AF: 0.389

Gnomad4 EAS AF: 0.409

Gnomad4 SAS AF: 0.377

Gnomad4 FIN AF: 0.310

Gnomad4 NFE AF: 0.292

Gnomad4 OTH AF: 0.458

Alfa AF: 0.372 Hom.: 3167

Bravo AF: 0.483

Asia WGS AF: 0.404 AC: 1408 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.93
DANN	Benign	0.59

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2367291; hg19: chr4-74730380;