rs2189555

chr7-11289374-C-T

Variant summary

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

The ENST00000421121.5(ENSG00000230333):n.113+36149C>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 0.102 in 151,878 control chromosomes in the GnomAD database, including 1,065 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 0.10 (1065 hom., cov: 32)
• Consequence: ENST00000421121.5 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0160

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.363 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
	ENST00000445839.5	n.246+36149C>T		intron_variant, non_coding_transcript_variant		4

Frequencies

GnomAD3 genomes AF: 0.102 AC: 15435 AN: 151758 Hom.: 1066 Cov.: 32

Gnomad AFR AF: 0.101

Gnomad AMI AF: 0.0526

Gnomad AMR AF: 0.145

Gnomad ASJ AF: 0.0704

Gnomad EAS AF: 0.377

Gnomad SAS AF: 0.123

Gnomad FIN AF: 0.131

Gnomad MID AF: 0.0924

Gnomad NFE AF: 0.0678

Gnomad OTH AF: 0.0983

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

GnomAD4 genome AF: 0.102 AC: 15457 AN: 151878 Hom.: 1065 Cov.: 32 AF XY: 0.107 AC XY: 7946 AN XY: 74212

Gnomad4 AFR AF: 0.102

Gnomad4 AMR AF: 0.145

Gnomad4 ASJ AF: 0.0704

Gnomad4 EAS AF: 0.377

Gnomad4 SAS AF: 0.122

Gnomad4 FIN AF: 0.131

Gnomad4 NFE AF: 0.0678

Gnomad4 OTH AF: 0.0982

Alfa AF: 0.0929 Hom.: 108

Bravo AF: 0.105

Asia WGS AF: 0.213 AC: 738 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
Cadd	Benign	8.3
Dann	Benign	0.78

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2189555; hg19: chr7-11329001;