6-90319078-T-C

Variant summary

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

The ENST00000667364.1(ENSG00000260271):n.30+23542T>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 0.286 in 152,162 control chromosomes in the GnomAD database, including 7,934 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 0.29 (7934 hom., cov: 33)
• Consequence: ENST00000667364.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.506

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.756 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105377891	XR_942778.4	n.499-12286T>C		intron_variant, non_coding_transcript_variant
LOC105377891	XR_007059677.1	n.498+21342T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000667364.1	n.30+23542T>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.287 AC: 43563 AN: 152044 Hom.: 7938 Cov.: 33

Gnomad AFR AF: 0.0915

Gnomad AMI AF: 0.227

Gnomad AMR AF: 0.338

Gnomad ASJ AF: 0.261

Gnomad EAS AF: 0.777

Gnomad SAS AF: 0.320

Gnomad FIN AF: 0.460

Gnomad MID AF: 0.274

Gnomad NFE AF: 0.329

Gnomad OTH AF: 0.302

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

GnomAD4 genome AF: 0.286 AC: 43566 AN: 152162 Hom.: 7934 Cov.: 33 AF XY: 0.296 AC XY: 22004 AN XY: 74360

Gnomad4 AFR AF: 0.0915

Gnomad4 AMR AF: 0.338

Gnomad4 ASJ AF: 0.261

Gnomad4 EAS AF: 0.776

Gnomad4 SAS AF: 0.320

Gnomad4 FIN AF: 0.460

Gnomad4 NFE AF: 0.329

Gnomad4 OTH AF: 0.301

Alfa AF: 0.319 Hom.: 10732

Bravo AF: 0.274

Asia WGS AF: 0.480 AC: 1666 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	0.35
Dann	Benign	0.56

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs285640; hg19: chr6-91028797; COSMIC: COSV60243431;