chr5-44709039-A-G

Variant names:

• chr5-44709039-A-G
• rs16901937

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.392 in 152,016 control chromosomes in the GnomAD database, including 12,066 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 0.39 (12066 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.13

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.489 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: 0.392 AC: 59535 AN: 151896 Hom.: 12042 Cov.: 32

Gnomad AFR AF: 0.322

Gnomad AMI AF: 0.331

Gnomad AMR AF: 0.451

Gnomad ASJ AF: 0.431

Gnomad EAS AF: 0.505

Gnomad SAS AF: 0.500

Gnomad FIN AF: 0.397

Gnomad MID AF: 0.443

Gnomad NFE AF: 0.403

Gnomad OTH AF: 0.404

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

GnomAD4 genome AF: 0.392 AC: 59581 AN: 152016 Hom.: 12066 Cov.: 32 AF XY: 0.398 AC XY: 29529 AN XY: 74280

Gnomad4 AFR AF: 0.321

Gnomad4 AMR AF: 0.452

Gnomad4 ASJ AF: 0.431

Gnomad4 EAS AF: 0.505

Gnomad4 SAS AF: 0.501

Gnomad4 FIN AF: 0.397

Gnomad4 NFE AF: 0.403

Gnomad4 OTH AF: 0.410

Alfa AF: 0.398 Hom.: 3501

Bravo AF: 0.392

Asia WGS AF: 0.508 AC: 1766 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	7.2
DANN	Benign	0.71

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs16901937; hg19: chr5-44709141;