7-80266903-T-C

Variant summary

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

The ENST00000447198.2(ENSG00000234223):n.203-3545A>G 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 0.153 in 152,036 control chromosomes in the GnomAD database, including 1,970 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 0.15 (1970 hom., cov: 32)
• Consequence: ENST00000447198.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.50

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.185 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
	ENST00000447198.2	n.203-3545A>G		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.153 AC: 23315 AN: 151918 Hom.: 1973 Cov.: 32

Gnomad AFR AF: 0.119

Gnomad AMI AF: 0.275

Gnomad AMR AF: 0.138

Gnomad ASJ AF: 0.238

Gnomad EAS AF: 0.00154

Gnomad SAS AF: 0.121

Gnomad FIN AF: 0.139

Gnomad MID AF: 0.266

Gnomad NFE AF: 0.187

Gnomad OTH AF: 0.165

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

GnomAD4 genome AF: 0.153 AC: 23310 AN: 152036 Hom.: 1970 Cov.: 32 AF XY: 0.149 AC XY: 11081 AN XY: 74330

Gnomad4 AFR AF: 0.119

Gnomad4 AMR AF: 0.138

Gnomad4 ASJ AF: 0.238

Gnomad4 EAS AF: 0.00154

Gnomad4 SAS AF: 0.121

Gnomad4 FIN AF: 0.139

Gnomad4 NFE AF: 0.187

Gnomad4 OTH AF: 0.163

Alfa AF: 0.161 Hom.: 1144

Bravo AF: 0.151

Asia WGS AF: 0.0620 AC: 217 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
Cadd	Benign	2.6
Dann	Benign	0.75

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs564127; hg19: chr7-79896219;