chr5-163417562-G-C

Variant names:

• chr5-163417562-G-C
• rs10515859
• ENST00000503504.2:n.375+8241C>G

Variant summary

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

The ENST00000509211.2(ENSG00000254186):​n.326-5179C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.426 in 152,012 control chromosomes in the GnomAD database, including 14,250 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 0.43 (14250 hom., cov: 32)
• Consequence: ENSG00000254186 ENST00000509211.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.27

Genes affected

ENSG00000254186 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.463 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105377700	XR_001742962.3	n.141-5179C>G		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000254186	ENST00000503504.2	n.375+8241C>G		intron_variant	Intron 3 of 4	5
ENSG00000254186	ENST00000503615.6	n.351+8241C>G		intron_variant	Intron 3 of 4	5
ENSG00000254186	ENST00000509211.2	n.326-5179C>G		intron_variant	Intron 2 of 5	3

Frequencies

GnomAD3 genomes AF: 0.426 AC: 64781 AN: 151894 Hom.: 14240 Cov.: 32

Gnomad AFR AF: 0.436

Gnomad AMI AF: 0.434

Gnomad AMR AF: 0.428

Gnomad ASJ AF: 0.399

Gnomad EAS AF: 0.0594

Gnomad SAS AF: 0.233

Gnomad FIN AF: 0.401

Gnomad MID AF: 0.389

Gnomad NFE AF: 0.467

Gnomad OTH AF: 0.439

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

GnomAD4 genome AF: 0.426 AC: 64816 AN: 152012 Hom.: 14250 Cov.: 32 AF XY: 0.418 AC XY: 31100 AN XY: 74340

African (AFR) AF: 0.435 AC: 18038 AN: 41434

American (AMR) AF: 0.427 AC: 6530 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.399 AC: 1381 AN: 3464

East Asian (EAS) AF: 0.0597 AC: 309 AN: 5172

South Asian (SAS) AF: 0.234 AC: 1127 AN: 4826

European-Finnish (FIN) AF: 0.401 AC: 4238 AN: 10568

Middle Eastern (MID) AF: 0.398 AC: 117 AN: 294

European-Non Finnish (NFE) AF: 0.467 AC: 31768 AN: 67960

Other (OTH) AF: 0.434 AC: 914 AN: 2104

Alfa AF: 0.456 Hom.: 2018

Bravo AF: 0.430

Asia WGS AF: 0.201 AC: 702 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	0.086
DANN	Benign	0.57
PhyloP100		-2.3

Splicing

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

Publications

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Other links and lift over

dbSNP: rs10515859; hg19: chr5-162844568;