rs7001413

chr8-74097998-G-T

Variant summary

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

The ENST00000519323.1(ENSG00000254288):n.304-1421G>T 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 0.0551 in 152,170 control chromosomes in the GnomAD database, including 413 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 0.055 (413 hom., cov: 32)
• Consequence: ENST00000519323.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.131

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.127 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LY96	XM_017013299.2	c.385-1421G>T		intron_variant
LY96	XM_017013300.2	c.295-1421G>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000519323.1	n.304-1421G>T		intron_variant, non_coding_transcript_variant		1
	ENST00000668834.1	n.175+4279G>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.0549 AC: 8347 AN: 152052 Hom.: 405 Cov.: 32

Gnomad AFR AF: 0.129

Gnomad AMI AF: 0.00110

Gnomad AMR AF: 0.0425

Gnomad ASJ AF: 0.0409

Gnomad EAS AF: 0.000192

Gnomad SAS AF: 0.00767

Gnomad FIN AF: 0.0375

Gnomad MID AF: 0.0316

Gnomad NFE AF: 0.0239

Gnomad OTH AF: 0.0602

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

GnomAD4 genome AF: 0.0551 AC: 8384 AN: 152170 Hom.: 413 Cov.: 32 AF XY: 0.0532 AC XY: 3957 AN XY: 74402

Gnomad4 AFR AF: 0.130

Gnomad4 AMR AF: 0.0423

Gnomad4 ASJ AF: 0.0409

Gnomad4 EAS AF: 0.000193

Gnomad4 SAS AF: 0.00768

Gnomad4 FIN AF: 0.0375

Gnomad4 NFE AF: 0.0239

Gnomad4 OTH AF: 0.0643

Alfa AF: 0.0309 Hom.: 105

Bravo AF: 0.0588

Asia WGS AF: 0.0290 AC: 99 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	3.0
Dann	Benign	0.34

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7001413; hg19: chr8-75010233;