chr7-127508578-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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105375490	XR_001745351.2	n.2349+603C>T		intron_variant	Intron 3 of 4
LOC105375490	XR_001745352.2	n.551+603C>T		intron_variant	Intron 4 of 5
LOC105375490	XR_007060511.1	n.232+603C>T		intron_variant	Intron 3 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000295686	ENST00000731796.1	n.70-3212C>T		intron_variant	Intron 1 of 2
ENSG00000295686	ENST00000731797.1	n.355-23296C>T		intron_variant	Intron 3 of 3
ENSG00000295686	ENST00000731798.1	n.244-3212C>T		intron_variant	Intron 3 of 4

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 v4.3

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

Other links and lift over

dbSNP: rs12668127; hg19: chr7-127148632;