5-170100638-C-T

Variant names:

• chr5-170100638-C-T
• rs1501644

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 0.274 in 152,094 control chromosomes in the GnomAD database, including 7,314 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 0.27 (7314 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0460
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.484 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: 0.274 AC: 41582 AN: 151976 Hom.: 7295 Cov.: 33

Gnomad AFR AF: 0.490

Gnomad AMI AF: 0.176

Gnomad AMR AF: 0.220

Gnomad ASJ AF: 0.193

Gnomad EAS AF: 0.469

Gnomad SAS AF: 0.242

Gnomad FIN AF: 0.195

Gnomad MID AF: 0.171

Gnomad NFE AF: 0.160

Gnomad OTH AF: 0.257

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

GnomAD4 genome AF: 0.274 AC: 41651 AN: 152094 Hom.: 7314 Cov.: 33 AF XY: 0.275 AC XY: 20420 AN XY: 74362

African (AFR) AF: 0.490 AC: 20308 AN: 41438

American (AMR) AF: 0.220 AC: 3361 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.193 AC: 669 AN: 3470

East Asian (EAS) AF: 0.469 AC: 2426 AN: 5172

South Asian (SAS) AF: 0.242 AC: 1167 AN: 4824

European-Finnish (FIN) AF: 0.195 AC: 2060 AN: 10590

Middle Eastern (MID) AF: 0.163 AC: 48 AN: 294

European-Non Finnish (NFE) AF: 0.160 AC: 10894 AN: 67990

Other (OTH) AF: 0.264 AC: 558 AN: 2112

Alfa AF: 0.195 Hom.: 3397

Bravo AF: 0.286

Asia WGS AF: 0.347 AC: 1206 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	3.1
DANN	Benign	0.29
PhyloP100		-0.046

Splicing

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

Other links and lift over

dbSNP: rs1501644; hg19: chr5-169527642;