11-69346225-G-T

Position:

• chr11-69346225-G-T

Variant summary

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

The ENST00000544781.5(ENSG00000260877):​n.324+4547G>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 0.153 in 152,134 control chromosomes in the GnomAD database, including 2,780 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 (2780 hom., cov: 32)
• Consequence: ENST00000544781.5 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.07

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.301 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105369370	XR_950269.4	n.466+4547G>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000544781.5	n.324+4547G>T		intron_variant, non_coding_transcript_variant		2
	ENST00000540356.1	n.123+4547G>T		intron_variant, non_coding_transcript_variant		3
	ENST00000541137.5	n.246+4547G>T		intron_variant, non_coding_transcript_variant		3
	ENST00000561588.3	n.169+4547G>T		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.153 AC: 23249 AN: 152016 Hom.: 2764 Cov.: 32

Gnomad AFR AF: 0.304

Gnomad AMI AF: 0.0384

Gnomad AMR AF: 0.219

Gnomad ASJ AF: 0.0709

Gnomad EAS AF: 0.313

Gnomad SAS AF: 0.114

Gnomad FIN AF: 0.0498

Gnomad MID AF: 0.0854

Gnomad NFE AF: 0.0594

Gnomad OTH AF: 0.141

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

GnomAD4 genome AF: 0.153 AC: 23314 AN: 152134 Hom.: 2780 Cov.: 32 AF XY: 0.154 AC XY: 11425 AN XY: 74386

Gnomad4 AFR AF: 0.305

Gnomad4 AMR AF: 0.219

Gnomad4 ASJ AF: 0.0709

Gnomad4 EAS AF: 0.314

Gnomad4 SAS AF: 0.113

Gnomad4 FIN AF: 0.0498

Gnomad4 NFE AF: 0.0594

Gnomad4 OTH AF: 0.144

Alfa AF: 0.0734 Hom.: 879

Bravo AF: 0.175

Asia WGS AF: 0.204 AC: 711 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.19
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: rs4584599; hg19: chr11-69160993;