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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105375490	XR_001745351.2	n.2793-7229G>C		intron_variant	Intron 4 of 4
LOC105375490	XR_001745352.2	n.995-7229G>C		intron_variant	Intron 5 of 5
LOC105375490	XR_007060511.1	n.676-7229G>C		intron_variant	Intron 4 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000295686	ENST00000731796.1	n.117-7229G>C		intron_variant	Intron 2 of 2
ENSG00000295686	ENST00000731797.1	n.355-7229G>C		intron_variant	Intron 3 of 3
ENSG00000295686	ENST00000731798.1	n.291-7229G>C		intron_variant	Intron 4 of 4

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 v4.3

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

Other links and lift over

dbSNP: rs1018852; hg19: chr7-127132565;