5-163831016-C-T

Variant names:

• chr5-163831016-C-T
• rs1421867

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.632 AC: 26204 AN: 41452

American (AMR) AF: 0.391 AC: 5983 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.423 AC: 1468 AN: 3472

East Asian (EAS) AF: 0.254 AC: 1307 AN: 5138

South Asian (SAS) AF: 0.195 AC: 942 AN: 4826

European-Finnish (FIN) AF: 0.335 AC: 3546 AN: 10574

Middle Eastern (MID) AF: 0.445 AC: 130 AN: 292

European-Non Finnish (NFE) AF: 0.371 AC: 25225 AN: 67950

Other (OTH) AF: 0.454 AC: 959 AN: 2114

Alfa AF: 0.412 Hom.: 2428

Bravo AF: 0.451

Asia WGS AF: 0.224 AC: 781 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.39
DANN	Benign	0.39
PhyloP100		-0.60

Splicing

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

Other links and lift over

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