2-175622240-C-T

Variant names:

• chr2-175622240-C-T
• rs9287986
• XR_007087312.1:n.11606G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XR_007087312.1(LOC107985962):​n.11606G>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.482 in 151,942 control chromosomes in the GnomAD database, including 18,074 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 0.48 (18074 hom., cov: 31)
• Consequence: LOC107985962 XR_007087312.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00900
• Publications: 2 publications found

Genes affected

LOC107985962 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 = 0.636 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC107985962	XR_007087312.1	n.11606G>A		non_coding_transcript_exon_variant	Exon 4 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000289349	ENST00000685522.2	n.463+27666C>T		intron_variant	Intron 1 of 2
ENSG00000289349	ENST00000692740.2	n.325+27666C>T		intron_variant	Intron 2 of 3
ENSG00000289349	ENST00000840653.1	n.271+27666C>T		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.482 AC: 73142 AN: 151824 Hom.: 18052 Cov.: 31

Gnomad AFR AF: 0.567

Gnomad AMI AF: 0.192

Gnomad AMR AF: 0.465

Gnomad ASJ AF: 0.469

Gnomad EAS AF: 0.430

Gnomad SAS AF: 0.656

Gnomad FIN AF: 0.493

Gnomad MID AF: 0.586

Gnomad NFE AF: 0.428

Gnomad OTH AF: 0.489

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

GnomAD4 genome AF: 0.482 AC: 73213 AN: 151942 Hom.: 18074 Cov.: 31 AF XY: 0.488 AC XY: 36215 AN XY: 74276

African (AFR) AF: 0.567 AC: 23490 AN: 41444

American (AMR) AF: 0.465 AC: 7101 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.469 AC: 1625 AN: 3468

East Asian (EAS) AF: 0.430 AC: 2218 AN: 5158

South Asian (SAS) AF: 0.655 AC: 3149 AN: 4804

European-Finnish (FIN) AF: 0.493 AC: 5214 AN: 10572

Middle Eastern (MID) AF: 0.579 AC: 169 AN: 292

European-Non Finnish (NFE) AF: 0.428 AC: 29044 AN: 67924

Other (OTH) AF: 0.487 AC: 1029 AN: 2114

Alfa AF: 0.450 Hom.: 6124

Bravo AF: 0.480

Asia WGS AF: 0.532 AC: 1850 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	5.5
DANN	Benign	0.76
PhyloP100		0.0090

Splicing

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

Other links and lift over

dbSNP: rs9287986; hg19: chr2-176486968;