5-171724227-T-C

Variant names:

• chr5-171724227-T-C
• rs10516089
• XR_001742983.2:n.1633+1677A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XR_001742983.2(LOC105377724):​n.1633+1677A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.351 in 152,068 control chromosomes in the GnomAD database, including 9,504 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 0.35 (9504 hom., cov: 32)
• Consequence: LOC105377724 XR_001742983.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.52
• Publications: 7 publications found

Genes affected

LOC105377724 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.393 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000803459.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000285914	ENST00000803459.1		n.*47A>G		downstream_gene	N/A
	ENSG00000285914	ENST00000803460.1		n.*41A>G		downstream_gene	N/A
	ENSG00000285914	ENST00000803461.1		n.*113A>G		downstream_gene	N/A

Frequencies

GnomAD3 genomes AF: 0.352 AC: 53419 AN: 151952 Hom.: 9496 Cov.: 32

Gnomad AFR AF: 0.399

Gnomad AMI AF: 0.313

Gnomad AMR AF: 0.374

Gnomad ASJ AF: 0.268

Gnomad EAS AF: 0.365

Gnomad SAS AF: 0.214

Gnomad FIN AF: 0.364

Gnomad MID AF: 0.316

Gnomad NFE AF: 0.330

Gnomad OTH AF: 0.347

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

GnomAD4 genome AF: 0.351 AC: 53444 AN: 152068 Hom.: 9504 Cov.: 32 AF XY: 0.352 AC XY: 26166 AN XY: 74332

African (AFR) AF: 0.398 AC: 16514 AN: 41472

American (AMR) AF: 0.374 AC: 5706 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.268 AC: 932 AN: 3472

East Asian (EAS) AF: 0.364 AC: 1881 AN: 5174

South Asian (SAS) AF: 0.215 AC: 1036 AN: 4818

European-Finnish (FIN) AF: 0.364 AC: 3841 AN: 10560

Middle Eastern (MID) AF: 0.310 AC: 91 AN: 294

European-Non Finnish (NFE) AF: 0.330 AC: 22428 AN: 67990

Other (OTH) AF: 0.345 AC: 730 AN: 2114

Alfa AF: 0.336 Hom.: 26282

Bravo AF: 0.358

Asia WGS AF: 0.259 AC: 903 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.9
DANN	Benign	0.74
PhyloP100		-1.5

Splicing

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

Other links and lift over

dbSNP: rs10516089; hg19: chr5-171151231;