rs161645

Variant names:

• chr5-104734216-A-G
• rs161645
• ENST00000503650.1:n.328+152642T>C

Your query was ambiguous. Multiple possible variants found:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 19 publications found

Genes affected

ENSG00000251574 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
LOC105379109	NR_188304.1	n.175+29064T>C		intron_variant	Intron 2 of 3
LOC105379109	NR_188305.1	n.295+29064T>C		intron_variant	Intron 2 of 3
LOC105379109	NR_188306.1	n.175+29064T>C		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000251574	ENST00000503650.1	n.328+152642T>C		intron_variant	Intron 2 of 2	3
ENSG00000251574	ENST00000505824.6	n.307+29064T>C		intron_variant	Intron 2 of 2	3
ENSG00000251574	ENST00000506976.6	n.203+29064T>C		intron_variant	Intron 2 of 3	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

African (AFR) AF: 0.936 AC: 38881 AN: 41528

American (AMR) AF: 0.784 AC: 11962 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.681 AC: 2362 AN: 3466

East Asian (EAS) AF: 0.924 AC: 4758 AN: 5150

South Asian (SAS) AF: 0.615 AC: 2965 AN: 4824

European-Finnish (FIN) AF: 0.727 AC: 7683 AN: 10564

Middle Eastern (MID) AF: 0.697 AC: 205 AN: 294

European-Non Finnish (NFE) AF: 0.676 AC: 45948 AN: 67944

Other (OTH) AF: 0.768 AC: 1623 AN: 2114

Alfa AF: 0.709 Hom.: 148535

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
PhyloP100		-0.93

Splicing

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

Other links and lift over

dbSNP: rs161645; hg19: chr5-104069917;