8-19793650-T-C

Variant names:

• chr8-19793650-T-C
• rs920590
• ENST00000773374.1:n.206-14586A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000773374.1(ENSG00000300677):​n.206-14586A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.389 in 151,744 control chromosomes in the GnomAD database, including 11,884 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 0.39 (11884 hom., cov: 32)
• Consequence: ENSG00000300677 ENST00000773374.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.40
• Publications: 16 publications found

Genes affected

ENSG00000300677 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.49 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000773374.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000300677	ENST00000773374.1		n.206-14586A>G		intron	N/A
	ENSG00000300677	ENST00000773375.1		n.54-885A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.389 AC: 59005 AN: 151626 Hom.: 11877 Cov.: 32

Gnomad AFR AF: 0.463

Gnomad AMI AF: 0.406

Gnomad AMR AF: 0.417

Gnomad ASJ AF: 0.513

Gnomad EAS AF: 0.451

Gnomad SAS AF: 0.506

Gnomad FIN AF: 0.279

Gnomad MID AF: 0.522

Gnomad NFE AF: 0.334

Gnomad OTH AF: 0.412

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

GnomAD4 genome AF: 0.389 AC: 59057 AN: 151744 Hom.: 11884 Cov.: 32 AF XY: 0.392 AC XY: 29031 AN XY: 74104

African (AFR) AF: 0.464 AC: 19167 AN: 41350

American (AMR) AF: 0.417 AC: 6351 AN: 15240

Ashkenazi Jewish (ASJ) AF: 0.513 AC: 1780 AN: 3472

East Asian (EAS) AF: 0.451 AC: 2313 AN: 5128

South Asian (SAS) AF: 0.507 AC: 2437 AN: 4806

European-Finnish (FIN) AF: 0.279 AC: 2937 AN: 10514

Middle Eastern (MID) AF: 0.527 AC: 155 AN: 294

European-Non Finnish (NFE) AF: 0.334 AC: 22687 AN: 67918

Other (OTH) AF: 0.408 AC: 860 AN: 2110

Alfa AF: 0.356 Hom.: 33626

Bravo AF: 0.400

Asia WGS AF: 0.481 AC: 1673 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.12
DANN	Benign	0.39
PhyloP100		-3.4

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs920590;

hg19: chr8-19651161;