rs517258

chr7-65278280-T-G

Variant summary

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

The ENST00000687368.1(ENSG00000282381):n.180+8742T>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 0.379 in 151,868 control chromosomes in the GnomAD database, including 11,093 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 0.38 (11093 hom., cov: 31)
• Consequence: ENST00000687368.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.883

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.73).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.405 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105375334	XR_001744938.2	n.165+8742T>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000687368.1	n.180+8742T>G		intron_variant, non_coding_transcript_variant
	ENST00000632111.1	n.165+8742T>G		intron_variant, non_coding_transcript_variant		2
	ENST00000685802.1	n.150+8742T>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.379 AC: 57439 AN: 151750 Hom.: 11078 Cov.: 31

Gnomad AFR AF: 0.410

Gnomad AMI AF: 0.300

Gnomad AMR AF: 0.294

Gnomad ASJ AF: 0.308

Gnomad EAS AF: 0.377

Gnomad SAS AF: 0.400

Gnomad FIN AF: 0.339

Gnomad MID AF: 0.437

Gnomad NFE AF: 0.388

Gnomad OTH AF: 0.363

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

GnomAD4 genome AF: 0.379 AC: 57489 AN: 151868 Hom.: 11093 Cov.: 31 AF XY: 0.374 AC XY: 27764 AN XY: 74224

Gnomad4 AFR AF: 0.410

Gnomad4 AMR AF: 0.294

Gnomad4 ASJ AF: 0.308

Gnomad4 EAS AF: 0.377

Gnomad4 SAS AF: 0.401

Gnomad4 FIN AF: 0.339

Gnomad4 NFE AF: 0.388

Gnomad4 OTH AF: 0.365

Alfa AF: 0.378 Hom.: 2855

Bravo AF: 0.374

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.73
Cadd	Benign	5.2

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs517258; hg19: chr7-64743183;