5-101281541-T-C

Variant names:

• chr5-101281541-T-C
• rs4415055

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 0.092 in 152,126 control chromosomes in the GnomAD database, including 1,374 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 0.092 (1374 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.80
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.224 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: 0.0918 AC: 13961 AN: 152008 Hom.: 1368 Cov.: 32

Gnomad AFR AF: 0.228

Gnomad AMI AF: 0.0143

Gnomad AMR AF: 0.161

Gnomad ASJ AF: 0.0236

Gnomad EAS AF: 0.00405

Gnomad SAS AF: 0.0280

Gnomad FIN AF: 0.00424

Gnomad MID AF: 0.0285

Gnomad NFE AF: 0.0235

Gnomad OTH AF: 0.0756

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

GnomAD4 genome AF: 0.0920 AC: 13997 AN: 152126 Hom.: 1374 Cov.: 32 AF XY: 0.0909 AC XY: 6762 AN XY: 74382

African (AFR) AF: 0.228 AC: 9467 AN: 41474

American (AMR) AF: 0.162 AC: 2465 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.0236 AC: 82 AN: 3470

East Asian (EAS) AF: 0.00406 AC: 21 AN: 5176

South Asian (SAS) AF: 0.0290 AC: 140 AN: 4822

European-Finnish (FIN) AF: 0.00424 AC: 45 AN: 10606

Middle Eastern (MID) AF: 0.0340 AC: 10 AN: 294

European-Non Finnish (NFE) AF: 0.0235 AC: 1596 AN: 68014

Other (OTH) AF: 0.0748 AC: 158 AN: 2112

Alfa AF: 0.0309 Hom.: 63

Bravo AF: 0.109

Asia WGS AF: 0.0370 AC: 129 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.26
DANN	Benign	0.67
PhyloP100		-1.8

Splicing

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

Other links and lift over

dbSNP: rs4415055; hg19: chr5-100617245;