rs1090817

Positions:

• chr2-31676400-T-A
• chr2-31676400-T-C

Variant summary

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

The XR_001739388.1(LOC107985862):​n.318-7956A>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 0.843 in 152,260 control chromosomes in the GnomAD database, including 54,370 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 0.84 (54370 hom., cov: 33)
• Consequence: LOC107985862 XR_001739388.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.279

Genes affected

LOC107985862 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.75).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.888 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC107985862	XR_001739388.1	n.318-7956A>T		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.844 AC: 128343 AN: 152142 Hom.: 54356 Cov.: 33

Gnomad AFR AF: 0.774

Gnomad AMI AF: 0.873

Gnomad AMR AF: 0.890

Gnomad ASJ AF: 0.735

Gnomad EAS AF: 0.910

Gnomad SAS AF: 0.872

Gnomad FIN AF: 0.867

Gnomad MID AF: 0.807

Gnomad NFE AF: 0.870

Gnomad OTH AF: 0.840

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

GnomAD4 genome AF: 0.843 AC: 128395 AN: 152260 Hom.: 54370 Cov.: 33 AF XY: 0.845 AC XY: 62900 AN XY: 74444

Gnomad4 AFR AF: 0.773

Gnomad4 AMR AF: 0.890

Gnomad4 ASJ AF: 0.735

Gnomad4 EAS AF: 0.910

Gnomad4 SAS AF: 0.872

Gnomad4 FIN AF: 0.867

Gnomad4 NFE AF: 0.870

Gnomad4 OTH AF: 0.840

Alfa AF: 0.854 Hom.: 6510

Bravo AF: 0.842

Asia WGS AF: 0.874 AC: 3038 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.75
CADD	Benign	9.7
DANN	Benign	0.77

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1090817; hg19: chr2-31901469;