rs2383393

Positions:

• chr4-179743500-A-G
• chr4-179743500-A-T

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 0.65 in 151,750 control chromosomes in the GnomAD database, including 32,524 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 0.65 (32524 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.261

ACMG classification

Verdict is Benign. Variant got -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 = 0.822 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.650 AC: 98502 AN: 151632 Hom.: 32479 Cov.: 32

Gnomad AFR AF: 0.723

Gnomad AMI AF: 0.625

Gnomad AMR AF: 0.655

Gnomad ASJ AF: 0.588

Gnomad EAS AF: 0.843

Gnomad SAS AF: 0.689

Gnomad FIN AF: 0.530

Gnomad MID AF: 0.725

Gnomad NFE AF: 0.608

Gnomad OTH AF: 0.663

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

GnomAD4 genome AF: 0.650 AC: 98605 AN: 151750 Hom.: 32524 Cov.: 32 AF XY: 0.651 AC XY: 48264 AN XY: 74134

Gnomad4 AFR AF: 0.723

Gnomad4 AMR AF: 0.654

Gnomad4 ASJ AF: 0.588

Gnomad4 EAS AF: 0.843

Gnomad4 SAS AF: 0.690

Gnomad4 FIN AF: 0.530

Gnomad4 NFE AF: 0.608

Gnomad4 OTH AF: 0.667

Alfa AF: 0.621 Hom.: 43192

Bravo AF: 0.662

Asia WGS AF: 0.740 AC: 2562 AN: 3458

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.30
DANN	Benign	0.47

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2383393; hg19: chr4-180664653;