rs1438673

chr5-111131801-C-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 0.608 in 152,094 control chromosomes in the GnomAD database, including 29,450 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 0.61 (29450 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.34

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.79 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: 0.608 AC: 92410 AN: 151976 Hom.: 29410 Cov.: 32

Gnomad AFR AF: 0.784

Gnomad AMI AF: 0.459

Gnomad AMR AF: 0.610

Gnomad ASJ AF: 0.532

Gnomad EAS AF: 0.570

Gnomad SAS AF: 0.811

Gnomad FIN AF: 0.573

Gnomad MID AF: 0.684

Gnomad NFE AF: 0.500

Gnomad OTH AF: 0.591

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

GnomAD4 genome AF: 0.608 AC: 92506 AN: 152094 Hom.: 29450 Cov.: 32 AF XY: 0.615 AC XY: 45710 AN XY: 74356

Gnomad4 AFR AF: 0.784

Gnomad4 AMR AF: 0.610

Gnomad4 ASJ AF: 0.532

Gnomad4 EAS AF: 0.570

Gnomad4 SAS AF: 0.811

Gnomad4 FIN AF: 0.573

Gnomad4 NFE AF: 0.500

Gnomad4 OTH AF: 0.591

Alfa AF: 0.572 Hom.: 2474

Bravo AF: 0.611

Asia WGS AF: 0.692 AC: 2402 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
Cadd	Benign	2.1
Dann	Benign	0.73

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1438673; hg19: chr5-110467499;