chr5-163831016-C-T

Variant names:

• chr5-163831016-C-T
• rs1421867

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 0.435 in 152,014 control chromosomes in the GnomAD database, including 15,538 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 0.43 (15538 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.605

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.626 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: 0.435 AC: 66067 AN: 151894 Hom.: 15525 Cov.: 32

Gnomad AFR AF: 0.633

Gnomad AMI AF: 0.373

Gnomad AMR AF: 0.392

Gnomad ASJ AF: 0.423

Gnomad EAS AF: 0.255

Gnomad SAS AF: 0.195

Gnomad FIN AF: 0.335

Gnomad MID AF: 0.443

Gnomad NFE AF: 0.371

Gnomad OTH AF: 0.459

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

GnomAD4 genome AF: 0.435 AC: 66104 AN: 152014 Hom.: 15538 Cov.: 32 AF XY: 0.429 AC XY: 31832 AN XY: 74280

Gnomad4 AFR AF: 0.632

Gnomad4 AMR AF: 0.391

Gnomad4 ASJ AF: 0.423

Gnomad4 EAS AF: 0.254

Gnomad4 SAS AF: 0.195

Gnomad4 FIN AF: 0.335

Gnomad4 NFE AF: 0.371

Gnomad4 OTH AF: 0.454

Alfa AF: 0.405 Hom.: 2268

Bravo AF: 0.451

Asia WGS AF: 0.224 AC: 781 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.39
DANN	Benign	0.39

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1421867; hg19: chr5-163258022; COSMIC: COSV60226850;