rs2203512

chr16-27045134-G-Achr16-27045134-G-T

Variant summary

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

The XR_950951.1(LOC105371153):n.859+400C>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 0.851 in 152,188 control chromosomes in the GnomAD database, including 55,472 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 0.85 (55472 hom., cov: 32)
• Consequence: LOC105371153 XR_950951.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.85

Genes affected

LOC105371153 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.904 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105371153	XR_950951.1	n.859+400C>T		intron_variant, non_coding_transcript_variant
LOC105371153	XR_001752325.1	n.2108+400C>T		intron_variant, non_coding_transcript_variant
LOC105371153	XR_001752326.1	n.1634+400C>T		intron_variant, non_coding_transcript_variant
LOC105371153	XR_001752327.1	n.2023-620C>T		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.851 AC: 129402 AN: 152070 Hom.: 55438 Cov.: 32

Gnomad AFR AF: 0.775

Gnomad AMI AF: 0.906

Gnomad AMR AF: 0.788

Gnomad ASJ AF: 0.881

Gnomad EAS AF: 0.685

Gnomad SAS AF: 0.822

Gnomad FIN AF: 0.938

Gnomad MID AF: 0.908

Gnomad NFE AF: 0.910

Gnomad OTH AF: 0.857

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

GnomAD4 genome AF: 0.851 AC: 129489 AN: 152188 Hom.: 55472 Cov.: 32 AF XY: 0.850 AC XY: 63253 AN XY: 74396

Gnomad4 AFR AF: 0.775

Gnomad4 AMR AF: 0.787

Gnomad4 ASJ AF: 0.881

Gnomad4 EAS AF: 0.686

Gnomad4 SAS AF: 0.822

Gnomad4 FIN AF: 0.938

Gnomad4 NFE AF: 0.910

Gnomad4 OTH AF: 0.858

Alfa AF: 0.888 Hom.: 88008

Bravo AF: 0.834

Asia WGS AF: 0.787 AC: 2736 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	0.40
Dann	Benign	0.20

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2203512; hg19: chr16-27056455;