rs11772451

Positions:

• chr7-15066869-G-C

Variant summary

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

The ENST00000445093.1(ENSG00000227489):​n.306+357G>C 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 0.39 in 151,728 control chromosomes in the GnomAD database, including 14,816 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 0.39 (14816 hom., cov: 32)
• Consequence: ENST00000445093.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.12

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.688 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000445093.1	n.306+357G>C		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.390 AC: 59123 AN: 151610 Hom.: 14771 Cov.: 32

Gnomad AFR AF: 0.694

Gnomad AMI AF: 0.157

Gnomad AMR AF: 0.380

Gnomad ASJ AF: 0.175

Gnomad EAS AF: 0.558

Gnomad SAS AF: 0.258

Gnomad FIN AF: 0.304

Gnomad MID AF: 0.263

Gnomad NFE AF: 0.233

Gnomad OTH AF: 0.334

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

GnomAD4 genome AF: 0.390 AC: 59218 AN: 151728 Hom.: 14816 Cov.: 32 AF XY: 0.394 AC XY: 29182 AN XY: 74160

Gnomad4 AFR AF: 0.695

Gnomad4 AMR AF: 0.380

Gnomad4 ASJ AF: 0.175

Gnomad4 EAS AF: 0.558

Gnomad4 SAS AF: 0.257

Gnomad4 FIN AF: 0.304

Gnomad4 NFE AF: 0.233

Gnomad4 OTH AF: 0.335

Alfa AF: 0.173 Hom.: 381

Bravo AF: 0.413

Asia WGS AF: 0.429 AC: 1486 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.23
DANN	Benign	0.38

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11772451; hg19: chr7-15106494;