rs775800

chr2-121055323-T-C

Variant summary

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

The XR_923264.2(LOC105373587):n.1030-1064T>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 0.354 in 152,006 control chromosomes in the GnomAD database, including 9,668 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 0.35 (9668 hom., cov: 31)
• Consequence: LOC105373587 XR_923264.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.944

Genes affected

LOC105373587 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.495 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105373587	XR_923264.2	n.1030-1064T>C		intron_variant, non_coding_transcript_variant
LOC105373587	XR_923265.2	n.230-1064T>C		intron_variant, non_coding_transcript_variant
LOC105373587	XR_923266.2	n.1030-1131T>C		intron_variant, non_coding_transcript_variant
LOC105373587	XR_923267.2	n.202-1064T>C		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.354 AC: 53735 AN: 151888 Hom.: 9657 Cov.: 31

Gnomad AFR AF: 0.332

Gnomad AMI AF: 0.313

Gnomad AMR AF: 0.378

Gnomad ASJ AF: 0.406

Gnomad EAS AF: 0.489

Gnomad SAS AF: 0.513

Gnomad FIN AF: 0.376

Gnomad MID AF: 0.354

Gnomad NFE AF: 0.334

Gnomad OTH AF: 0.358

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

GnomAD4 genome AF: 0.354 AC: 53773 AN: 152006 Hom.: 9668 Cov.: 31 AF XY: 0.360 AC XY: 26722 AN XY: 74288

Gnomad4 AFR AF: 0.332

Gnomad4 AMR AF: 0.379

Gnomad4 ASJ AF: 0.406

Gnomad4 EAS AF: 0.489

Gnomad4 SAS AF: 0.512

Gnomad4 FIN AF: 0.376

Gnomad4 NFE AF: 0.334

Gnomad4 OTH AF: 0.356

Alfa AF: 0.352 Hom.: 4863

Bravo AF: 0.353

Asia WGS AF: 0.491 AC: 1707 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
Cadd	Benign	7.0
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: rs775800; hg19: chr2-121812899;