5-69166611-C-T

Variant summary

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

The ENST00000690195.2(ENSG00000248664):n.79+260G>A 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 0.619 in 150,920 control chromosomes in the GnomAD database, including 29,734 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 0.62 (29734 hom., cov: 27)
• Consequence: ENST00000690195.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.547

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.76 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000690195.2	n.79+260G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.619 AC: 93314 AN: 150808 Hom.: 29684 Cov.: 27

Gnomad AFR AF: 0.766

Gnomad AMI AF: 0.662

Gnomad AMR AF: 0.641

Gnomad ASJ AF: 0.524

Gnomad EAS AF: 0.699

Gnomad SAS AF: 0.676

Gnomad FIN AF: 0.566

Gnomad MID AF: 0.585

Gnomad NFE AF: 0.528

Gnomad OTH AF: 0.597

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

GnomAD4 genome AF: 0.619 AC: 93425 AN: 150920 Hom.: 29734 Cov.: 27 AF XY: 0.624 AC XY: 45892 AN XY: 73580

Gnomad4 AFR AF: 0.767

Gnomad4 AMR AF: 0.641

Gnomad4 ASJ AF: 0.524

Gnomad4 EAS AF: 0.699

Gnomad4 SAS AF: 0.675

Gnomad4 FIN AF: 0.566

Gnomad4 NFE AF: 0.528

Gnomad4 OTH AF: 0.601

Alfa AF: 0.584 Hom.: 3862

Bravo AF: 0.627

Asia WGS AF: 0.700 AC: 2437 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
Cadd	Benign	5.9
Dann	Benign	0.80

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs350104; hg19: chr5-68462438;