7-109734977-G-T

Variant names:

• chr7-109734977-G-T
• rs711517
• ENST00000830489.1:n.196-18389C>A

Variant summary

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

The ENST00000830489.1(ENSG00000308019):​n.196-18389C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.8 in 152,136 control chromosomes in the GnomAD database, including 48,805 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 0.80 (48805 hom., cov: 32)
• Consequence: ENSG00000308019 ENST00000830489.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.90
• Publications: 4 publications found

Genes affected

ENSG00000308019 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.06).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.819 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000830489.1. 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
	ENSG00000308019	ENST00000830489.1		n.196-18389C>A		intron	N/A
	ENSG00000308019	ENST00000830490.1		n.184-18389C>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.800 AC: 121555 AN: 152018 Hom.: 48773 Cov.: 32

Gnomad AFR AF: 0.742

Gnomad AMI AF: 0.907

Gnomad AMR AF: 0.828

Gnomad ASJ AF: 0.761

Gnomad EAS AF: 0.815

Gnomad SAS AF: 0.769

Gnomad FIN AF: 0.835

Gnomad MID AF: 0.756

Gnomad NFE AF: 0.824

Gnomad OTH AF: 0.795

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

GnomAD4 genome AF: 0.800 AC: 121640 AN: 152136 Hom.: 48805 Cov.: 32 AF XY: 0.800 AC XY: 59502 AN XY: 74380

African (AFR) AF: 0.742 AC: 30783 AN: 41466

American (AMR) AF: 0.828 AC: 12657 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.761 AC: 2642 AN: 3472

East Asian (EAS) AF: 0.815 AC: 4216 AN: 5176

South Asian (SAS) AF: 0.769 AC: 3705 AN: 4820

European-Finnish (FIN) AF: 0.835 AC: 8859 AN: 10606

Middle Eastern (MID) AF: 0.759 AC: 223 AN: 294

European-Non Finnish (NFE) AF: 0.824 AC: 56060 AN: 68004

Other (OTH) AF: 0.791 AC: 1670 AN: 2110

Alfa AF: 0.812 Hom.: 24466

Bravo AF: 0.794

Asia WGS AF: 0.776 AC: 2698 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.12
DANN	Benign	0.31
PhyloP100		-2.9

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: rs711517;

hg19: chr7-109375034;