rs11265198

chr1-159450517-G-Achr1-159450517-G-Cchr1-159450517-G-T

Variant summary

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

The ENST00000431862.1(ENSG00000228560):n.227+18325C>T variant causes a intron, non coding transcript change. The variant allele was found at a frequency of 0.803 in 151,410 control chromosomes in the GnomAD database, including 54,353 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 0.80 (54353 hom., cov: 29)
• Consequence: ENST00000431862.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: No conservation score assigned

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.977 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
	ENST00000431862.1	n.227+18325C>T		intron_variant, non_coding_transcript_variant		1

Frequencies

GnomAD3 genomes AF: 0.804 AC: 121620 AN: 151318 Hom.: 54351 Cov.: 29

Gnomad AFR AF: 0.367

Gnomad AMI AF: 0.999

Gnomad AMR AF: 0.915

Gnomad ASJ AF: 0.950

Gnomad EAS AF: 1.00

Gnomad SAS AF: 0.973

Gnomad FIN AF: 0.989

Gnomad MID AF: 0.873

Gnomad NFE AF: 0.974

Gnomad OTH AF: 0.848

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

GnomAD4 genome AF: 0.803 AC: 121647 AN: 151410 Hom.: 54353 Cov.: 29 AF XY: 0.809 AC XY: 59873 AN XY: 73986

Gnomad4 AFR AF: 0.367

Gnomad4 AMR AF: 0.915

Gnomad4 ASJ AF: 0.950

Gnomad4 EAS AF: 1.00

Gnomad4 SAS AF: 0.973

Gnomad4 FIN AF: 0.989

Gnomad4 NFE AF: 0.974

Gnomad4 OTH AF: 0.849

Alfa AF: 0.804 Hom.: 10052

Bravo AF: 0.778

Asia WGS AF: 0.951 AC: 3307 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
Cadd	Benign	0.63
Dann	Benign	0.34

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11265198; hg19: chr1-159420307;