chr5-44148028-A-T

Variant names:

• chr5-44148028-A-T
• rs13358399

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 0.17 in 152,052 control chromosomes in the GnomAD database, including 2,336 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 0.17 (2336 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.232
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AMR) 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: 0.170 AC: 25865 AN: 151934 Hom.: 2332 Cov.: 32

Gnomad AFR AF: 0.196

Gnomad AMI AF: 0.182

Gnomad AMR AF: 0.231

Gnomad ASJ AF: 0.116

Gnomad EAS AF: 0.230

Gnomad SAS AF: 0.216

Gnomad FIN AF: 0.171

Gnomad MID AF: 0.161

Gnomad NFE AF: 0.136

Gnomad OTH AF: 0.158

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

GnomAD4 genome AF: 0.170 AC: 25904 AN: 152052 Hom.: 2336 Cov.: 32 AF XY: 0.172 AC XY: 12758 AN XY: 74316

African (AFR) AF: 0.196 AC: 8156 AN: 41508

American (AMR) AF: 0.231 AC: 3516 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.116 AC: 403 AN: 3470

East Asian (EAS) AF: 0.228 AC: 1179 AN: 5164

South Asian (SAS) AF: 0.216 AC: 1043 AN: 4830

European-Finnish (FIN) AF: 0.171 AC: 1803 AN: 10564

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

European-Non Finnish (NFE) AF: 0.136 AC: 9247 AN: 67944

Other (OTH) AF: 0.162 AC: 343 AN: 2116

Alfa AF: 0.0763 Hom.: 88

Bravo AF: 0.178

Asia WGS AF: 0.256 AC: 885 AN: 3458

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.1
DANN	Benign	0.67
PhyloP100		0.23

Splicing

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

Other links and lift over

dbSNP: rs13358399; hg19: chr5-44148130;