rs1483274

Positions:

• chr11-103728869-G-A
• chr11-103728869-G-C

Variant summary

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

The ENST00000533459.1(ENSG00000254987):​n.128-23971C>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 0.927 in 152,200 control chromosomes in the GnomAD database, including 65,936 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 0.93 (65936 hom., cov: 30)
• Consequence: ENST00000533459.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.08

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.978 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
	ENST00000533459.1	n.128-23971C>T		intron_variant, non_coding_transcript_variant		4

Frequencies

GnomAD3 genomes AF: 0.928 AC: 141071 AN: 152082 Hom.: 65897 Cov.: 30

Gnomad AFR AF: 0.810

Gnomad AMI AF: 0.998

Gnomad AMR AF: 0.956

Gnomad ASJ AF: 0.987

Gnomad EAS AF: 0.831

Gnomad SAS AF: 0.948

Gnomad FIN AF: 0.990

Gnomad MID AF: 0.946

Gnomad NFE AF: 0.984

Gnomad OTH AF: 0.934

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

GnomAD4 genome AF: 0.927 AC: 141164 AN: 152200 Hom.: 65936 Cov.: 30 AF XY: 0.929 AC XY: 69111 AN XY: 74420

Gnomad4 AFR AF: 0.810

Gnomad4 AMR AF: 0.956

Gnomad4 ASJ AF: 0.987

Gnomad4 EAS AF: 0.832

Gnomad4 SAS AF: 0.948

Gnomad4 FIN AF: 0.990

Gnomad4 NFE AF: 0.984

Gnomad4 OTH AF: 0.936

Alfa AF: 0.953 Hom.: 9351

Bravo AF: 0.919

Asia WGS AF: 0.895 AC: 3115 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.13
DANN	Benign	0.33

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1483274; hg19: chr11-103599597;