11-33895919-A-T

Position:

• chr11-33895919-A-T

Variant summary

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

The XR_931176.3(LOC105376621):​n.90+1884A>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 0.648 in 152,066 control chromosomes in the GnomAD database, including 34,750 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 0.65 (34750 hom., cov: 32)
• Consequence: LOC105376621 XR_931176.3 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.523

Genes affected

LOC105376621 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.786 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105376621	XR_931176.3	n.90+1884A>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.648 AC: 98500 AN: 151950 Hom.: 34757 Cov.: 32

Gnomad AFR AF: 0.357

Gnomad AMI AF: 0.904

Gnomad AMR AF: 0.622

Gnomad ASJ AF: 0.705

Gnomad EAS AF: 0.607

Gnomad SAS AF: 0.716

Gnomad FIN AF: 0.845

Gnomad MID AF: 0.699

Gnomad NFE AF: 0.792

Gnomad OTH AF: 0.658

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

GnomAD4 genome AF: 0.648 AC: 98502 AN: 152066 Hom.: 34750 Cov.: 32 AF XY: 0.650 AC XY: 48290 AN XY: 74346

Gnomad4 AFR AF: 0.357

Gnomad4 AMR AF: 0.622

Gnomad4 ASJ AF: 0.705

Gnomad4 EAS AF: 0.607

Gnomad4 SAS AF: 0.716

Gnomad4 FIN AF: 0.845

Gnomad4 NFE AF: 0.792

Gnomad4 OTH AF: 0.652

Alfa AF: 0.712 Hom.: 5008

Bravo AF: 0.619

Asia WGS AF: 0.588 AC: 2048 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	11
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: rs750781; hg19: chr11-33917466;