rs12707249

chr7-135794825-C-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, non coding transcript 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: ENST00000419211.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.368

Genes affected

(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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000419211.2	n.595+19710C>T		intron_variant, non_coding_transcript_variant		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;