rs2173946

Positions:

• chr5-5910544-G-A

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 0.338 in 152,044 control chromosomes in the GnomAD database, including 8,936 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 0.34 (8936 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.76

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.396 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.339 AC: 51428 AN: 151924 Hom.: 8928 Cov.: 32

Gnomad AFR AF: 0.317

Gnomad AMI AF: 0.488

Gnomad AMR AF: 0.288

Gnomad ASJ AF: 0.305

Gnomad EAS AF: 0.410

Gnomad SAS AF: 0.275

Gnomad FIN AF: 0.299

Gnomad MID AF: 0.225

Gnomad NFE AF: 0.370

Gnomad OTH AF: 0.303

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

GnomAD4 genome AF: 0.338 AC: 51459 AN: 152044 Hom.: 8936 Cov.: 32 AF XY: 0.333 AC XY: 24724 AN XY: 74320

Gnomad4 AFR AF: 0.317

Gnomad4 AMR AF: 0.288

Gnomad4 ASJ AF: 0.305

Gnomad4 EAS AF: 0.411

Gnomad4 SAS AF: 0.275

Gnomad4 FIN AF: 0.299

Gnomad4 NFE AF: 0.370

Gnomad4 OTH AF: 0.302

Alfa AF: 0.357 Hom.: 17265

Bravo AF: 0.339

Asia WGS AF: 0.335 AC: 1167 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.047
DANN	Benign	0.66

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2173946; hg19: chr5-5910657;