chr5-170188494-T-C

Variant names:

• chr5-170188494-T-C
• rs1054998

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 0.351 in 152,046 control chromosomes in the GnomAD database, including 9,757 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 0.35 (9757 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.339
• Publications: 5 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.399 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: 0.351 AC: 53260 AN: 151928 Hom.: 9736 Cov.: 32

Gnomad AFR AF: 0.282

Gnomad AMI AF: 0.215

Gnomad AMR AF: 0.407

Gnomad ASJ AF: 0.440

Gnomad EAS AF: 0.147

Gnomad SAS AF: 0.388

Gnomad FIN AF: 0.391

Gnomad MID AF: 0.459

Gnomad NFE AF: 0.382

Gnomad OTH AF: 0.379

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

GnomAD4 genome AF: 0.351 AC: 53321 AN: 152046 Hom.: 9757 Cov.: 32 AF XY: 0.351 AC XY: 26078 AN XY: 74318

African (AFR) AF: 0.283 AC: 11720 AN: 41480

American (AMR) AF: 0.407 AC: 6221 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.440 AC: 1529 AN: 3472

East Asian (EAS) AF: 0.147 AC: 757 AN: 5154

South Asian (SAS) AF: 0.388 AC: 1872 AN: 4824

European-Finnish (FIN) AF: 0.391 AC: 4126 AN: 10560

Middle Eastern (MID) AF: 0.473 AC: 139 AN: 294

European-Non Finnish (NFE) AF: 0.382 AC: 25967 AN: 67966

Other (OTH) AF: 0.376 AC: 794 AN: 2110

Alfa AF: 0.375 Hom.: 33911

Bravo AF: 0.349

Asia WGS AF: 0.310 AC: 1080 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	3.4
DANN	Benign	0.55
PhyloP100		-0.34

Splicing

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

Other links and lift over

dbSNP: rs1054998; hg19: chr5-169615498; COSMIC: COSV72584169;