rs1116180

Positions:

• chr5-44442841-T-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 0.154 in 151,804 control chromosomes in the GnomAD database, including 2,041 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 0.15 (2041 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.442

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.23 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: 0.154 AC: 23427 AN: 151686 Hom.: 2031 Cov.: 32

Gnomad AFR AF: 0.233

Gnomad AMI AF: 0.0758

Gnomad AMR AF: 0.131

Gnomad ASJ AF: 0.233

Gnomad EAS AF: 0.118

Gnomad SAS AF: 0.112

Gnomad FIN AF: 0.113

Gnomad MID AF: 0.170

Gnomad NFE AF: 0.121

Gnomad OTH AF: 0.153

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

GnomAD4 genome AF: 0.154 AC: 23452 AN: 151804 Hom.: 2041 Cov.: 32 AF XY: 0.154 AC XY: 11403 AN XY: 74180

Gnomad4 AFR AF: 0.234

Gnomad4 AMR AF: 0.130

Gnomad4 ASJ AF: 0.233

Gnomad4 EAS AF: 0.118

Gnomad4 SAS AF: 0.111

Gnomad4 FIN AF: 0.113

Gnomad4 NFE AF: 0.121

Gnomad4 OTH AF: 0.152

Alfa AF: 0.142 Hom.: 216

Bravo AF: 0.161

Asia WGS AF: 0.128 AC: 439 AN: 3450

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	3.5
DANN	Benign	0.30

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1116180; hg19: chr5-44442943;