rs7463110

chr8-33979515-A-Cchr8-33979515-A-Gchr8-33979515-A-T

Variant summary

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

The ENST00000521714.1(ENSG00000254194):n.172-3972T>G 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 0.534 in 151,924 control chromosomes in the GnomAD database, including 22,024 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 0.53 (22024 hom., cov: 32)
• Consequence: ENST00000521714.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.169

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.805 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105379364	XR_002956701.2	n.288-28341A>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000521714.1	n.172-3972T>G		intron_variant, non_coding_transcript_variant		2
	ENST00000523063.5	n.505-28341A>C		intron_variant, non_coding_transcript_variant		3
	ENST00000518163.5	n.72-3972T>G		intron_variant, non_coding_transcript_variant		3
	ENST00000523336.2	n.148-28341A>C		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.534 AC: 81108 AN: 151806 Hom.: 22011 Cov.: 32

Gnomad AFR AF: 0.501

Gnomad AMI AF: 0.552

Gnomad AMR AF: 0.547

Gnomad ASJ AF: 0.398

Gnomad EAS AF: 0.825

Gnomad SAS AF: 0.686

Gnomad FIN AF: 0.512

Gnomad MID AF: 0.386

Gnomad NFE AF: 0.531

Gnomad OTH AF: 0.499

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

GnomAD4 genome AF: 0.534 AC: 81153 AN: 151924 Hom.: 22024 Cov.: 32 AF XY: 0.536 AC XY: 39772 AN XY: 74268

Gnomad4 AFR AF: 0.501

Gnomad4 AMR AF: 0.547

Gnomad4 ASJ AF: 0.398

Gnomad4 EAS AF: 0.825

Gnomad4 SAS AF: 0.686

Gnomad4 FIN AF: 0.512

Gnomad4 NFE AF: 0.531

Gnomad4 OTH AF: 0.501

Alfa AF: 0.514 Hom.: 4837

Bravo AF: 0.532

Asia WGS AF: 0.723 AC: 2511 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
Cadd	Benign	7.0
Dann	Benign	0.57

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7463110; hg19: chr8-33837033;