5-123856740-T-C

Variant names:

• chr5-123856740-T-C
• rs1021769

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 0.595 in 152,060 control chromosomes in the GnomAD database, including 28,003 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 0.60 (28003 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.227

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• 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: 0.595 AC: 90456 AN: 151942 Hom.: 27972 Cov.: 33

Gnomad AFR AF: 0.767

Gnomad AMI AF: 0.654

Gnomad AMR AF: 0.546

Gnomad ASJ AF: 0.605

Gnomad EAS AF: 0.555

Gnomad SAS AF: 0.486

Gnomad FIN AF: 0.464

Gnomad MID AF: 0.671

Gnomad NFE AF: 0.531

Gnomad OTH AF: 0.603

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

GnomAD4 genome AF: 0.595 AC: 90531 AN: 152060 Hom.: 28003 Cov.: 33 AF XY: 0.587 AC XY: 43599 AN XY: 74310

Gnomad4 AFR AF: 0.767

Gnomad4 AMR AF: 0.546

Gnomad4 ASJ AF: 0.605

Gnomad4 EAS AF: 0.556

Gnomad4 SAS AF: 0.486

Gnomad4 FIN AF: 0.464

Gnomad4 NFE AF: 0.531

Gnomad4 OTH AF: 0.600

Alfa AF: 0.547 Hom.: 32520

Bravo AF: 0.612

Asia WGS AF: 0.525 AC: 1827 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	4.0
DANN	Benign	0.86

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1021769; hg19: chr5-123192434; COSMIC: COSV60192378;