rs10817678

Variant names:

• chr9-114817177-G-A
• rs10817678
• ENST00000776746.1:n.453+1042C>T

Variant summary

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

The ENST00000776746.1(ENSG00000301160):​n.453+1042C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.735 in 152,088 control chromosomes in the GnomAD database, including 42,033 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 0.74 (42033 hom., cov: 32)
• Consequence: ENSG00000301160 ENST00000776746.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.408
• Publications: 11 publications found

Genes affected

ENSG00000301160 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.877 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000776746.1. 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
	ENSG00000301160	ENST00000776746.1		n.453+1042C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.735 AC: 111736 AN: 151970 Hom.: 41981 Cov.: 32

Gnomad AFR AF: 0.884

Gnomad AMI AF: 0.602

Gnomad AMR AF: 0.741

Gnomad ASJ AF: 0.756

Gnomad EAS AF: 0.503

Gnomad SAS AF: 0.729

Gnomad FIN AF: 0.687

Gnomad MID AF: 0.734

Gnomad NFE AF: 0.670

Gnomad OTH AF: 0.713

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

GnomAD4 genome AF: 0.735 AC: 111850 AN: 152088 Hom.: 42033 Cov.: 32 AF XY: 0.735 AC XY: 54632 AN XY: 74338

African (AFR) AF: 0.885 AC: 36720 AN: 41514

American (AMR) AF: 0.740 AC: 11317 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.756 AC: 2622 AN: 3468

East Asian (EAS) AF: 0.503 AC: 2595 AN: 5156

South Asian (SAS) AF: 0.729 AC: 3516 AN: 4820

European-Finnish (FIN) AF: 0.687 AC: 7261 AN: 10564

Middle Eastern (MID) AF: 0.748 AC: 220 AN: 294

European-Non Finnish (NFE) AF: 0.670 AC: 45540 AN: 67962

Other (OTH) AF: 0.715 AC: 1511 AN: 2114

Alfa AF: 0.731 Hom.: 5910

Bravo AF: 0.743

Asia WGS AF: 0.665 AC: 2312 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.31
DANN	Benign	0.62
PhyloP100		-0.41

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: rs10817678;

hg19: chr9-117579457;