6-110957720-G-C

Variant names:

• chr6-110957720-G-C
• rs9487562
• ENST00000758068.1:n.129+1318C>G

Variant summary

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

The ENST00000758068.1(ENSG00000298809):​n.129+1318C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.14 in 142,376 control chromosomes in the GnomAD database, including 1,734 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 0.14 (1734 hom., cov: 32)
• Consequence: ENSG00000298809 ENST00000758068.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.46
• Publications: 0 publications found

Genes affected

ENSG00000298809 (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 = 0.25 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000758068.1. 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
	ENSG00000298809	ENST00000758068.1		n.129+1318C>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.140 AC: 19876 AN: 142256 Hom.: 1727 Cov.: 32

Gnomad AFR AF: 0.253

Gnomad AMI AF: 0.0637

Gnomad AMR AF: 0.0889

Gnomad ASJ AF: 0.141

Gnomad EAS AF: 0.0514

Gnomad SAS AF: 0.153

Gnomad FIN AF: 0.0592

Gnomad MID AF: 0.176

Gnomad NFE AF: 0.0944

Gnomad OTH AF: 0.136

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

GnomAD4 genome AF: 0.140 AC: 19930 AN: 142376 Hom.: 1734 Cov.: 32 AF XY: 0.138 AC XY: 9566 AN XY: 69186

African (AFR) AF: 0.254 AC: 10334 AN: 40724

American (AMR) AF: 0.0888 AC: 1296 AN: 14596

Ashkenazi Jewish (ASJ) AF: 0.141 AC: 481 AN: 3420

East Asian (EAS) AF: 0.0508 AC: 96 AN: 1888

South Asian (SAS) AF: 0.152 AC: 660 AN: 4330

European-Finnish (FIN) AF: 0.0592 AC: 561 AN: 9474

Middle Eastern (MID) AF: 0.172 AC: 50 AN: 290

European-Non Finnish (NFE) AF: 0.0944 AC: 6131 AN: 64930

Other (OTH) AF: 0.138 AC: 274 AN: 1986

Alfa AF: 0.0367 Hom.: 29

Bravo AF: 0.174

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.89
DANN	Benign	0.17
PhyloP100		-1.5

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: rs9487562;

hg19: chr6-111278923;