7-127508578-G-A

Variant names:

• chr7-127508578-G-A
• rs12668127
• ENST00000731796.1:n.70-3212C>T

Variant summary

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

The ENST00000731796.1(ENSG00000295686):​n.70-3212C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.325 in 152,044 control chromosomes in the GnomAD database, including 10,067 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 0.32 (10067 hom., cov: 32)
• Consequence: ENSG00000295686 ENST00000731796.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.981
• Publications: 5 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=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.69 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.70-3212C>T		intron	N/A
	ENSG00000295686	ENST00000731797.1		n.355-23296C>T		intron	N/A
	ENSG00000295686	ENST00000731798.1		n.244-3212C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.325 AC: 49340 AN: 151926 Hom.: 10055 Cov.: 32

Gnomad AFR AF: 0.0905

Gnomad AMI AF: 0.401

Gnomad AMR AF: 0.374

Gnomad ASJ AF: 0.268

Gnomad EAS AF: 0.710

Gnomad SAS AF: 0.414

Gnomad FIN AF: 0.460

Gnomad MID AF: 0.225

Gnomad NFE AF: 0.402

Gnomad OTH AF: 0.323

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

GnomAD4 genome AF: 0.325 AC: 49351 AN: 152044 Hom.: 10067 Cov.: 32 AF XY: 0.333 AC XY: 24760 AN XY: 74322

African (AFR) AF: 0.0903 AC: 3746 AN: 41502

American (AMR) AF: 0.375 AC: 5720 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.268 AC: 930 AN: 3472

East Asian (EAS) AF: 0.709 AC: 3661 AN: 5160

South Asian (SAS) AF: 0.416 AC: 2003 AN: 4816

European-Finnish (FIN) AF: 0.460 AC: 4856 AN: 10564

Middle Eastern (MID) AF: 0.218 AC: 64 AN: 294

European-Non Finnish (NFE) AF: 0.402 AC: 27321 AN: 67946

Other (OTH) AF: 0.324 AC: 685 AN: 2114

Alfa AF: 0.356 Hom.: 22784

Bravo AF: 0.308

Asia WGS AF: 0.506 AC: 1754 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.067
DANN	Benign	0.68
PhyloP100		-0.98

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: rs12668127;

hg19: chr7-127148632;