rs2964475

chr5-5407701-T-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000669435.2(ENSG00000286753):n.817+13050A>C variant causes a intron, non coding transcript 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: ENST00000669435.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.220

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt
LOC101929200	XR_001742583.3	n.817+13050A>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000669435.2	n.817+13050A>C		intron_variant, non_coding_transcript_variant
	ENST00000686499.1	n.817+13050A>C		intron_variant, non_coding_transcript_variant
	ENST00000690642.1	n.903+10324A>C		intron_variant, non_coding_transcript_variant
	ENST00000693678.1	n.329+13050A>C		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.549

Gnomad4 AMR AF: 0.521

Gnomad4 ASJ AF: 0.596

Gnomad4 EAS AF: 0.488

Gnomad4 SAS AF: 0.694

Gnomad4 FIN AF: 0.625

Gnomad4 NFE AF: 0.608

Gnomad4 OTH AF: 0.568

Alfa AF: 0.591 Hom.: 26272

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2964475; hg19: chr5-5407814;