rs7138744

Variant names:

• chr12-26853027-A-G
• rs7138744
• ENST00000766166.1:n.142+6690A>G

Variant summary

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

The ENST00000766166.1(ENSG00000299765):​n.142+6690A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.295 in 152,058 control chromosomes in the GnomAD database, including 6,670 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 0.29 (6670 hom., cov: 31)
• Consequence: ENSG00000299765 ENST00000766166.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.88
• Publications: 2 publications found

Genes affected

ENSG00000299765 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.321 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000299765	ENST00000766166.1	n.142+6690A>G		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.295 AC: 44792 AN: 151940 Hom.: 6658 Cov.: 31

Gnomad AFR AF: 0.278

Gnomad AMI AF: 0.356

Gnomad AMR AF: 0.259

Gnomad ASJ AF: 0.322

Gnomad EAS AF: 0.287

Gnomad SAS AF: 0.336

Gnomad FIN AF: 0.282

Gnomad MID AF: 0.354

Gnomad NFE AF: 0.311

Gnomad OTH AF: 0.268

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

GnomAD4 genome AF: 0.295 AC: 44840 AN: 152058 Hom.: 6670 Cov.: 31 AF XY: 0.292 AC XY: 21738 AN XY: 74318

African (AFR) AF: 0.279 AC: 11555 AN: 41490

American (AMR) AF: 0.259 AC: 3951 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.322 AC: 1118 AN: 3472

East Asian (EAS) AF: 0.287 AC: 1487 AN: 5178

South Asian (SAS) AF: 0.335 AC: 1612 AN: 4816

European-Finnish (FIN) AF: 0.282 AC: 2980 AN: 10558

Middle Eastern (MID) AF: 0.350 AC: 103 AN: 294

European-Non Finnish (NFE) AF: 0.311 AC: 21141 AN: 67956

Other (OTH) AF: 0.270 AC: 568 AN: 2106

Alfa AF: 0.306 Hom.: 10418

Bravo AF: 0.297

Asia WGS AF: 0.315 AC: 1099 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.12
DANN	Benign	0.35
PhyloP100		-1.9

Splicing

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

Other links and lift over

dbSNP: rs7138744; hg19: chr12-27005960; COSMIC: COSV101081819;