8-16786917-G-A

Position:

• chr8-16786917-G-A

Variant summary

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

The ENST00000521411.2(ENSG00000253496):​n.279-3635C>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 0.65 in 152,014 control chromosomes in the GnomAD database, including 32,617 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 0.65 (32617 hom., cov: 32)
• Consequence: ENST00000521411.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.200

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.755 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105379297	XR_949525.1	n.158-3635C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000521411.2	n.279-3635C>T		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.650 AC: 98684 AN: 151894 Hom.: 32571 Cov.: 32

Gnomad AFR AF: 0.735

Gnomad AMI AF: 0.654

Gnomad AMR AF: 0.713

Gnomad ASJ AF: 0.624

Gnomad EAS AF: 0.775

Gnomad SAS AF: 0.703

Gnomad FIN AF: 0.613

Gnomad MID AF: 0.630

Gnomad NFE AF: 0.577

Gnomad OTH AF: 0.635

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

GnomAD4 genome AF: 0.650 AC: 98787 AN: 152014 Hom.: 32617 Cov.: 32 AF XY: 0.655 AC XY: 48655 AN XY: 74318

Gnomad4 AFR AF: 0.736

Gnomad4 AMR AF: 0.714

Gnomad4 ASJ AF: 0.624

Gnomad4 EAS AF: 0.775

Gnomad4 SAS AF: 0.703

Gnomad4 FIN AF: 0.613

Gnomad4 NFE AF: 0.577

Gnomad4 OTH AF: 0.639

Alfa AF: 0.597 Hom.: 37633

Bravo AF: 0.659

Asia WGS AF: 0.758 AC: 2637 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.82
DANN	Benign	0.48

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs521882; hg19: chr8-16644426;