chr5-123870341-T-C

Position:

• chr5-123870341-T-C

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 0.73 in 152,168 control chromosomes in the GnomAD database, including 40,940 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 0.73 (40940 hom., cov: 33)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.721

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.751 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.123870341T>C		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.730 AC: 110983 AN: 152050 Hom.: 40898 Cov.: 33

Gnomad AFR AF: 0.722

Gnomad AMI AF: 0.614

Gnomad AMR AF: 0.763

Gnomad ASJ AF: 0.747

Gnomad EAS AF: 0.398

Gnomad SAS AF: 0.694

Gnomad FIN AF: 0.728

Gnomad MID AF: 0.661

Gnomad NFE AF: 0.757

Gnomad OTH AF: 0.730

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

GnomAD4 genome AF: 0.730 AC: 111075 AN: 152168 Hom.: 40940 Cov.: 33 AF XY: 0.728 AC XY: 54120 AN XY: 74390

Gnomad4 AFR AF: 0.722

Gnomad4 AMR AF: 0.762

Gnomad4 ASJ AF: 0.747

Gnomad4 EAS AF: 0.398

Gnomad4 SAS AF: 0.695

Gnomad4 FIN AF: 0.728

Gnomad4 NFE AF: 0.757

Gnomad4 OTH AF: 0.734

Alfa AF: 0.752 Hom.: 5369

Bravo AF: 0.730

Asia WGS AF: 0.617 AC: 2148 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.2
DANN	Benign	0.71

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs330678; hg19: chr5-123206035;