chr5-111131801-C-T

Variant names:

• chr5-111131801-C-T
• rs1438673

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;