7-127510196-T-C

Variant names:

• chr7-127510196-T-C
• rs11768389
• ENST00000731796.1:n.70-4830A>G

Variant summary

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

The ENST00000731796.1(ENSG00000295686):​n.70-4830A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.268 in 151,136 control chromosomes in the GnomAD database, including 7,057 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 0.27 (7057 hom., cov: 31)
• Consequence: ENSG00000295686 ENST00000731796.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.293
• 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=-0.82).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.634 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105375490	XR_001745351.2	n.2292-958A>G		intron_variant	Intron 2 of 4
LOC105375490	XR_001745352.2	n.494-958A>G		intron_variant	Intron 3 of 5
LOC105375490	XR_007060511.1	n.175-958A>G		intron_variant	Intron 2 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000295686	ENST00000731796.1	n.70-4830A>G		intron_variant	Intron 1 of 2
ENSG00000295686	ENST00000731797.1	n.355-24914A>G		intron_variant	Intron 3 of 3
ENSG00000295686	ENST00000731798.1	n.244-4830A>G		intron_variant	Intron 3 of 4

Frequencies

GnomAD3 genomes AF: 0.268 AC: 40461 AN: 151038 Hom.: 7053 Cov.: 31

Gnomad AFR AF: 0.0658

Gnomad AMI AF: 0.385

Gnomad AMR AF: 0.298

Gnomad ASJ AF: 0.195

Gnomad EAS AF: 0.653

Gnomad SAS AF: 0.314

Gnomad FIN AF: 0.425

Gnomad MID AF: 0.140

Gnomad NFE AF: 0.330

Gnomad OTH AF: 0.259

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

GnomAD4 genome AF: 0.268 AC: 40463 AN: 151136 Hom.: 7057 Cov.: 31 AF XY: 0.276 AC XY: 20375 AN XY: 73818

African (AFR) AF: 0.0657 AC: 2702 AN: 41148

American (AMR) AF: 0.298 AC: 4525 AN: 15186

Ashkenazi Jewish (ASJ) AF: 0.195 AC: 676 AN: 3458

East Asian (EAS) AF: 0.653 AC: 3357 AN: 5142

South Asian (SAS) AF: 0.315 AC: 1504 AN: 4778

European-Finnish (FIN) AF: 0.425 AC: 4386 AN: 10318

Middle Eastern (MID) AF: 0.130 AC: 37 AN: 284

European-Non Finnish (NFE) AF: 0.330 AC: 22380 AN: 67814

Other (OTH) AF: 0.260 AC: 547 AN: 2102

Alfa AF: 0.277 Hom.: 1825

Bravo AF: 0.251

Asia WGS AF: 0.437 AC: 1516 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	3.7
DANN	Benign	0.75
PhyloP100		0.29

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs11768389; hg19: chr7-127150250;