rs161645

Positions:

• chr5-104734216-A-G
• chr5-104734216-A-T

Variant summary

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

The ENST00000503650.1(ENSG00000251574):​n.328+152642T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.769 in 152,044 control chromosomes in the GnomAD database, including 46,128 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 0.77 (46128 hom., cov: 32)
• Consequence: ENSG00000251574 ENST00000503650.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.934

Genes affected

ENSG00000251574 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.928 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105379109	NR_188304.1	n.175+29064T>C		intron_variant
LOC105379109	NR_188305.1	n.295+29064T>C		intron_variant
LOC105379109	NR_188306.1	n.175+29064T>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000251574	ENST00000503650.1	n.328+152642T>C		intron_variant		3
ENSG00000251574	ENST00000505824.6	n.307+29064T>C		intron_variant		3
ENSG00000251574	ENST00000506976.6	n.203+29064T>C		intron_variant		3

Frequencies

GnomAD3 genomes AF: 0.769 AC: 116783 AN: 151924 Hom.: 46070 Cov.: 32

Gnomad AFR AF: 0.936

Gnomad AMI AF: 0.563

Gnomad AMR AF: 0.784

Gnomad ASJ AF: 0.681

Gnomad EAS AF: 0.923

Gnomad SAS AF: 0.616

Gnomad FIN AF: 0.727

Gnomad MID AF: 0.709

Gnomad NFE AF: 0.676

Gnomad OTH AF: 0.765

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

GnomAD4 genome AF: 0.769 AC: 116899 AN: 152044 Hom.: 46128 Cov.: 32 AF XY: 0.770 AC XY: 57167 AN XY: 74288

Gnomad4 AFR AF: 0.936

Gnomad4 AMR AF: 0.784

Gnomad4 ASJ AF: 0.681

Gnomad4 EAS AF: 0.924

Gnomad4 SAS AF: 0.615

Gnomad4 FIN AF: 0.727

Gnomad4 NFE AF: 0.676

Gnomad4 OTH AF: 0.768

Alfa AF: 0.696 Hom.: 60767

Bravo AF: 0.787

Asia WGS AF: 0.790 AC: 2747 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.63
DANN	Benign	0.56

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs161645; hg19: chr5-104069917;