rs7586564

Variant names:

• chr2-19588450-C-T
• rs7586564
• XR_001739315.1:n.2716G>A

Variant summary

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

The XR_001739315.1(LOC105373459):​n.2716G>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 0.198 in 152,164 control chromosomes in the GnomAD database, including 3,247 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 0.20 (3247 hom., cov: 32)
• Consequence: LOC105373459 XR_001739315.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.437
• Publications: 2 publications found

Genes affected

LOC105373459 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.265 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105373459	XR_001739315.1	n.2716G>A		non_coding_transcript_exon_variant	Exon 3 of 3
LOC105373459	XR_939780.2	n.2292G>A		non_coding_transcript_exon_variant	Exon 4 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000306962	ENST00000822227.1	n.248+35112G>A		intron_variant	Intron 2 of 4

Frequencies

GnomAD3 genomes AF: 0.198 AC: 30083 AN: 152046 Hom.: 3249 Cov.: 32

Gnomad AFR AF: 0.117

Gnomad AMI AF: 0.432

Gnomad AMR AF: 0.194

Gnomad ASJ AF: 0.187

Gnomad EAS AF: 0.158

Gnomad SAS AF: 0.278

Gnomad FIN AF: 0.248

Gnomad MID AF: 0.197

Gnomad NFE AF: 0.235

Gnomad OTH AF: 0.188

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

GnomAD4 genome AF: 0.198 AC: 30086 AN: 152164 Hom.: 3247 Cov.: 32 AF XY: 0.200 AC XY: 14851 AN XY: 74360

African (AFR) AF: 0.116 AC: 4836 AN: 41532

American (AMR) AF: 0.194 AC: 2962 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.187 AC: 648 AN: 3470

East Asian (EAS) AF: 0.159 AC: 821 AN: 5170

South Asian (SAS) AF: 0.277 AC: 1336 AN: 4824

European-Finnish (FIN) AF: 0.248 AC: 2620 AN: 10568

Middle Eastern (MID) AF: 0.199 AC: 58 AN: 292

European-Non Finnish (NFE) AF: 0.235 AC: 16014 AN: 68002

Other (OTH) AF: 0.188 AC: 397 AN: 2114

Alfa AF: 0.224 Hom.: 4641

Bravo AF: 0.189

Asia WGS AF: 0.172 AC: 602 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	2.1
DANN	Benign	0.43
PhyloP100		-0.44

Splicing

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

Other links and lift over

dbSNP: rs7586564; hg19: chr2-19788211;