7-127492511-C-G

Variant names:

• chr7-127492511-C-G
• rs1018852
• ENST00000731796.1:n.117-7229G>C

Variant summary

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

The ENST00000731796.1(ENSG00000295686):​n.117-7229G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.699 in 152,050 control chromosomes in the GnomAD database, including 37,489 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 0.70 (37489 hom., cov: 33)
• Consequence: ENSG00000295686 ENST00000731796.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.923
• Publications: 2 publications found

Genes affected

ENSG00000295686 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.927 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000731796.1. 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
	ENSG00000295686	ENST00000731796.1		n.117-7229G>C		intron	N/A
	ENSG00000295686	ENST00000731797.1		n.355-7229G>C		intron	N/A
	ENSG00000295686	ENST00000731798.1		n.291-7229G>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.699 AC: 106162 AN: 151934 Hom.: 37452 Cov.: 33

Gnomad AFR AF: 0.680

Gnomad AMI AF: 0.727

Gnomad AMR AF: 0.647

Gnomad ASJ AF: 0.632

Gnomad EAS AF: 0.949

Gnomad SAS AF: 0.713

Gnomad FIN AF: 0.800

Gnomad MID AF: 0.642

Gnomad NFE AF: 0.689

Gnomad OTH AF: 0.692

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

GnomAD4 genome AF: 0.699 AC: 106244 AN: 152050 Hom.: 37489 Cov.: 33 AF XY: 0.706 AC XY: 52499 AN XY: 74326

African (AFR) AF: 0.680 AC: 28222 AN: 41476

American (AMR) AF: 0.647 AC: 9901 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.632 AC: 2192 AN: 3470

East Asian (EAS) AF: 0.949 AC: 4927 AN: 5190

South Asian (SAS) AF: 0.713 AC: 3431 AN: 4810

European-Finnish (FIN) AF: 0.800 AC: 8454 AN: 10572

Middle Eastern (MID) AF: 0.629 AC: 185 AN: 294

European-Non Finnish (NFE) AF: 0.689 AC: 46818 AN: 67918

Other (OTH) AF: 0.688 AC: 1451 AN: 2108

Alfa AF: 0.699 Hom.: 4656

Bravo AF: 0.684

Asia WGS AF: 0.792 AC: 2742 AN: 3464

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.29
DANN	Benign	0.78
PhyloP100		-0.92

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: rs1018852;

hg19: chr7-127132565;