ENST00000781717.1:n.105+221C>T

Variant names:

• chr8-24942229-G-A
• rs6557786
• ENST00000781717.1:n.105+221C>T

Variant summary

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

The ENST00000781717.1(ENSG00000301773):​n.105+221C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.854 in 149,766 control chromosomes in the GnomAD database, including 54,634 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 0.85 (54634 hom., cov: 23)
• Consequence: ENSG00000301773 ENST00000781717.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.95
• Publications: 6 publications found

Genes affected

ENSG00000301773 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.956 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000781717.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000301773	ENST00000781717.1		n.105+221C>T		intron	N/A
	ENSG00000301773	ENST00000781718.1		n.-234C>T		upstream_gene	N/A
	ENSG00000301773	ENST00000781720.1		n.-234C>T		upstream_gene	N/A

Frequencies

GnomAD3 genomes AF: 0.854 AC: 127752 AN: 149648 Hom.: 54605 Cov.: 23

Gnomad AFR AF: 0.851

Gnomad AMI AF: 0.872

Gnomad AMR AF: 0.882

Gnomad ASJ AF: 0.849

Gnomad EAS AF: 0.978

Gnomad SAS AF: 0.910

Gnomad FIN AF: 0.804

Gnomad MID AF: 0.861

Gnomad NFE AF: 0.843

Gnomad OTH AF: 0.861

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

GnomAD4 genome AF: 0.854 AC: 127829 AN: 149766 Hom.: 54634 Cov.: 23 AF XY: 0.855 AC XY: 62384 AN XY: 72988

African (AFR) AF: 0.850 AC: 34489 AN: 40572

American (AMR) AF: 0.882 AC: 13264 AN: 15038

Ashkenazi Jewish (ASJ) AF: 0.849 AC: 2940 AN: 3464

East Asian (EAS) AF: 0.979 AC: 4887 AN: 4994

South Asian (SAS) AF: 0.910 AC: 4175 AN: 4588

European-Finnish (FIN) AF: 0.804 AC: 8280 AN: 10300

Middle Eastern (MID) AF: 0.867 AC: 255 AN: 294

European-Non Finnish (NFE) AF: 0.843 AC: 56972 AN: 67550

Other (OTH) AF: 0.863 AC: 1777 AN: 2060

Alfa AF: 0.851 Hom.: 211860

Bravo AF: 0.861

Asia WGS AF: 0.923 AC: 3210 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.80
DANN	Benign	0.80
PhyloP100		-1.9

Splicing

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

Other links and lift over

dbSNP: rs6557786; hg19: chr8-24799742;