chr5-5407701-T-G

Variant names:

• chr5-5407701-T-G
• rs2964475
• ENST00000669435.3:n.1028+13050A>C

Variant summary

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

The ENST00000669435.3(ENSG00000286753):​n.1028+13050A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.582 in 152,050 control chromosomes in the GnomAD database, including 25,825 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 0.58 (25825 hom., cov: 32)
• Consequence: ENSG00000286753 ENST00000669435.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.220
• Publications: 4 publications found

Genes affected

ENSG00000286753 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.674 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC101929200	XR_001742583.3	n.817+13050A>C		intron_variant	Intron 2 of 5
LOC101929200	XR_001742584.3	n.817+13050A>C		intron_variant	Intron 2 of 3
LOC101929200	XR_007059118.1	n.817+13050A>C		intron_variant	Intron 2 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000286753	ENST00000669435.3	n.1028+13050A>C		intron_variant	Intron 2 of 2
ENSG00000286753	ENST00000686499.1	n.817+13050A>C		intron_variant	Intron 2 of 3
ENSG00000286753	ENST00000690642.2	n.904+10324A>C		intron_variant	Intron 3 of 4

Frequencies

GnomAD3 genomes AF: 0.582 AC: 88405 AN: 151932 Hom.: 25813 Cov.: 32

Gnomad AFR AF: 0.549

Gnomad AMI AF: 0.530

Gnomad AMR AF: 0.522

Gnomad ASJ AF: 0.596

Gnomad EAS AF: 0.489

Gnomad SAS AF: 0.692

Gnomad FIN AF: 0.625

Gnomad MID AF: 0.655

Gnomad NFE AF: 0.608

Gnomad OTH AF: 0.566

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

GnomAD4 genome AF: 0.582 AC: 88454 AN: 152050 Hom.: 25825 Cov.: 32 AF XY: 0.584 AC XY: 43438 AN XY: 74322

African (AFR) AF: 0.549 AC: 22764 AN: 41454

American (AMR) AF: 0.521 AC: 7965 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.596 AC: 2068 AN: 3470

East Asian (EAS) AF: 0.488 AC: 2522 AN: 5164

South Asian (SAS) AF: 0.694 AC: 3334 AN: 4806

European-Finnish (FIN) AF: 0.625 AC: 6615 AN: 10578

Middle Eastern (MID) AF: 0.646 AC: 190 AN: 294

European-Non Finnish (NFE) AF: 0.608 AC: 41314 AN: 67980

Other (OTH) AF: 0.568 AC: 1201 AN: 2114

Alfa AF: 0.589 Hom.: 38475

Bravo AF: 0.572

Asia WGS AF: 0.605 AC: 2101 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	1.9
DANN	Benign	0.65
PhyloP100		-0.22

Splicing

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

Other links and lift over

dbSNP: rs2964475; hg19: chr5-5407814;