rs12707249

Variant names:

• chr7-135794825-C-T
• rs12707249
• ENST00000419211.2:n.595+19710C>T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000419211.2(ENSG00000224746):​n.595+19710C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.207 in 152,172 control chromosomes in the GnomAD database, including 3,845 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 0.21 (3845 hom., cov: 33)
• Consequence: ENSG00000224746 ENST00000419211.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.368

Genes affected

ENSG00000224746 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.324 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
ENSG00000224746	ENST00000419211.2	n.595+19710C>T		intron_variant	Intron 1 of 2	2

Frequencies

GnomAD3 genomes AF: 0.207 AC: 31411 AN: 152052 Hom.: 3814 Cov.: 33

Gnomad AFR AF: 0.328

Gnomad AMI AF: 0.111

Gnomad AMR AF: 0.279

Gnomad ASJ AF: 0.119

Gnomad EAS AF: 0.187

Gnomad SAS AF: 0.129

Gnomad FIN AF: 0.100

Gnomad MID AF: 0.159

Gnomad NFE AF: 0.146

Gnomad OTH AF: 0.205

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

GnomAD4 genome AF: 0.207 AC: 31497 AN: 152172 Hom.: 3845 Cov.: 33 AF XY: 0.203 AC XY: 15138 AN XY: 74398

Gnomad4 AFR AF: 0.329

Gnomad4 AMR AF: 0.280

Gnomad4 ASJ AF: 0.119

Gnomad4 EAS AF: 0.188

Gnomad4 SAS AF: 0.129

Gnomad4 FIN AF: 0.100

Gnomad4 NFE AF: 0.146

Gnomad4 OTH AF: 0.209

Alfa AF: 0.162 Hom.: 1814

Bravo AF: 0.226

Asia WGS AF: 0.196 AC: 681 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.0
DANN	Benign	0.65

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12707249; hg19: chr7-135479573;