5-141845881-C-A

Variant names:

• chr5-141845881-C-A
• rs57450513

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The variant allele was found at a frequency of 0.0151 in 149,184 control chromosomes in the GnomAD database, including 20 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 0.015 (20 hom., cov: 26)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.213
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BS1: Variant frequency is greater than expected in population amr. GnomAd4 allele frequency = 0.0151 (2260/149184) while in subpopulation AMR AF = 0.0281 (417/14840). AF 95% confidence interval is 0.0259. There are 20 homozygotes in GnomAd4. There are 1079 alleles in the male GnomAd4 subpopulation. Median coverage is 26. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 20 gene

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: 0.0152 AC: 2262 AN: 149072 Hom.: 20 Cov.: 26

Gnomad AFR AF: 0.00936

Gnomad AMI AF: 0.00554

Gnomad AMR AF: 0.0281

Gnomad ASJ AF: 0.00609

Gnomad EAS AF: 0.000392

Gnomad SAS AF: 0.00522

Gnomad FIN AF: 0.0131

Gnomad MID AF: 0.0222

Gnomad NFE AF: 0.0183

Gnomad OTH AF: 0.0202

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

GnomAD4 genome AF: 0.0151 AC: 2260 AN: 149184 Hom.: 20 Cov.: 26 AF XY: 0.0148 AC XY: 1079 AN XY: 72766

African (AFR) AF: 0.00931 AC: 375 AN: 40284

American (AMR) AF: 0.0281 AC: 417 AN: 14840

Ashkenazi Jewish (ASJ) AF: 0.00609 AC: 21 AN: 3448

East Asian (EAS) AF: 0.000393 AC: 2 AN: 5092

South Asian (SAS) AF: 0.00501 AC: 23 AN: 4594

European-Finnish (FIN) AF: 0.0131 AC: 136 AN: 10394

Middle Eastern (MID) AF: 0.0238 AC: 7 AN: 294

European-Non Finnish (NFE) AF: 0.0183 AC: 1233 AN: 67280

Other (OTH) AF: 0.0199 AC: 41 AN: 2056

Alfa AF: 0.0180 Hom.: 35

Asia WGS AF: 0.00375 AC: 13 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	9.7
DANN	Benign	0.72
PhyloP100		-0.21

Splicing

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

Other links and lift over

dbSNP: rs57450513; hg19: chr5-141225446;