5-159980157-A-C

Position:

• chr5-159980157-A-C

Variant summary

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

The XM_006714821.4(ADRA1B):​c.950-5514A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.139 in 151,896 control chromosomes in the GnomAD database, including 2,327 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 0.14 (2327 hom., cov: 31)
• Consequence: ADRA1B XM_006714821.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0980

Genes affected

ADRA1B (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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 = 0.303 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ADRA1B	XM_006714821.4	c.950-5514A>C		intron_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.139 AC: 21052 AN: 151778 Hom.: 2314 Cov.: 31

Gnomad AFR AF: 0.307

Gnomad AMI AF: 0.0802

Gnomad AMR AF: 0.0976

Gnomad ASJ AF: 0.0845

Gnomad EAS AF: 0.144

Gnomad SAS AF: 0.0981

Gnomad FIN AF: 0.0388

Gnomad MID AF: 0.174

Gnomad NFE AF: 0.0679

Gnomad OTH AF: 0.123

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

GnomAD4 genome AF: 0.139 AC: 21113 AN: 151896 Hom.: 2327 Cov.: 31 AF XY: 0.136 AC XY: 10080 AN XY: 74248

Gnomad4 AFR AF: 0.307

Gnomad4 AMR AF: 0.0975

Gnomad4 ASJ AF: 0.0845

Gnomad4 EAS AF: 0.145

Gnomad4 SAS AF: 0.0980

Gnomad4 FIN AF: 0.0388

Gnomad4 NFE AF: 0.0680

Gnomad4 OTH AF: 0.124

Alfa AF: 0.0838 Hom.: 975

Bravo AF: 0.151

Asia WGS AF: 0.151 AC: 526 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.1
DANN	Benign	0.45

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10053468; hg19: chr5-159407164;