rs869214

Positions:

• chr2-234605853-A-G
• chr2-234605853-A-T

Variant summary

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

The XR_923998.3(LOC105373936):​n.477-8043T>C 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 0.655 in 151,728 control chromosomes in the GnomAD database, including 33,835 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 0.66 (33835 hom., cov: 30)
• Consequence: LOC105373936 XR_923998.3 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0950

Genes affected

LOC105373936 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.844 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105373936	XR_923998.3	n.477-8043T>C		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.655 AC: 99307 AN: 151608 Hom.: 33799 Cov.: 30

Gnomad AFR AF: 0.852

Gnomad AMI AF: 0.516

Gnomad AMR AF: 0.616

Gnomad ASJ AF: 0.576

Gnomad EAS AF: 0.735

Gnomad SAS AF: 0.605

Gnomad FIN AF: 0.495

Gnomad MID AF: 0.669

Gnomad NFE AF: 0.572

Gnomad OTH AF: 0.654

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

GnomAD4 genome AF: 0.655 AC: 99396 AN: 151728 Hom.: 33835 Cov.: 30 AF XY: 0.651 AC XY: 48202 AN XY: 74088

Gnomad4 AFR AF: 0.852

Gnomad4 AMR AF: 0.616

Gnomad4 ASJ AF: 0.576

Gnomad4 EAS AF: 0.735

Gnomad4 SAS AF: 0.607

Gnomad4 FIN AF: 0.495

Gnomad4 NFE AF: 0.572

Gnomad4 OTH AF: 0.654

Alfa AF: 0.580 Hom.: 12885

Bravo AF: 0.673

Asia WGS AF: 0.638 AC: 2223 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.6
DANN	Benign	0.54

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs869214; hg19: chr2-235514497;