rs37554

Positions:

• chr5-82927814-A-C
• chr5-82927814-A-G
• chr5-82927814-A-T

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 0.739 in 152,000 control chromosomes in the GnomAD database, including 43,503 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 0.74 (43503 hom., cov: 32)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.566

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.84 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.82927814A>C		intergenic_region
LOC105379051	NR_188290.1	n.374-6701T>G		intron_variant
LOC105379051	NR_188291.1	n.374-6701T>G		intron_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.740 AC: 112359 AN: 151882 Hom.: 43503 Cov.: 32

Gnomad AFR AF: 0.491

Gnomad AMI AF: 0.865

Gnomad AMR AF: 0.789

Gnomad ASJ AF: 0.731

Gnomad EAS AF: 0.747

Gnomad SAS AF: 0.728

Gnomad FIN AF: 0.947

Gnomad MID AF: 0.715

Gnomad NFE AF: 0.846

Gnomad OTH AF: 0.748

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

GnomAD4 genome AF: 0.739 AC: 112395 AN: 152000 Hom.: 43503 Cov.: 32 AF XY: 0.744 AC XY: 55301 AN XY: 74282

Gnomad4 AFR AF: 0.491

Gnomad4 AMR AF: 0.789

Gnomad4 ASJ AF: 0.731

Gnomad4 EAS AF: 0.746

Gnomad4 SAS AF: 0.728

Gnomad4 FIN AF: 0.947

Gnomad4 NFE AF: 0.846

Gnomad4 OTH AF: 0.747

Alfa AF: 0.815 Hom.: 39187

Bravo AF: 0.715

Asia WGS AF: 0.708 AC: 2461 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	11
DANN	Benign	0.81

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs37554; hg19: chr5-82223633;