chr5-164190860-T-C

Variant names:

• chr5-164190860-T-C
• rs7703210
• ENST00000521805.1:n.495+3285A>G

Variant summary

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

The ENST00000521805.1(ENSG00000253331):​n.495+3285A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.568 in 151,812 control chromosomes in the GnomAD database, including 24,671 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 0.57 (24671 hom., cov: 32)
• Consequence: ENSG00000253331 ENST00000521805.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.147
• Publications: 2 publications found

Genes affected

ENSG00000253331 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.683 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000253331	ENST00000521805.1	n.495+3285A>G		intron_variant	Intron 4 of 4	3

Frequencies

GnomAD3 genomes AF: 0.568 AC: 86233 AN: 151696 Hom.: 24656 Cov.: 32

Gnomad AFR AF: 0.642

Gnomad AMI AF: 0.495

Gnomad AMR AF: 0.527

Gnomad ASJ AF: 0.576

Gnomad EAS AF: 0.703

Gnomad SAS AF: 0.630

Gnomad FIN AF: 0.505

Gnomad MID AF: 0.519

Gnomad NFE AF: 0.529

Gnomad OTH AF: 0.566

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

GnomAD4 genome AF: 0.568 AC: 86274 AN: 151812 Hom.: 24671 Cov.: 32 AF XY: 0.567 AC XY: 42065 AN XY: 74196

African (AFR) AF: 0.642 AC: 26560 AN: 41392

American (AMR) AF: 0.527 AC: 8033 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.576 AC: 1997 AN: 3470

East Asian (EAS) AF: 0.703 AC: 3607 AN: 5134

South Asian (SAS) AF: 0.631 AC: 3034 AN: 4812

European-Finnish (FIN) AF: 0.505 AC: 5314 AN: 10516

Middle Eastern (MID) AF: 0.514 AC: 151 AN: 294

European-Non Finnish (NFE) AF: 0.529 AC: 35926 AN: 67916

Other (OTH) AF: 0.568 AC: 1201 AN: 2116

Alfa AF: 0.571 Hom.: 3697

Bravo AF: 0.574

Asia WGS AF: 0.642 AC: 2230 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	1.9
DANN	Benign	0.58
PhyloP100		-0.15

Splicing

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

Other links and lift over

dbSNP: rs7703210; hg19: chr5-163617866;