2-184464964-G-A

Variant names:

• chr2-184464964-G-A
• rs768352
• XR_923656.1:n.233-1260G>A

Variant summary

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

The XR_923656.1(LOC105373779):​n.233-1260G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.348 in 151,894 control chromosomes in the GnomAD database, including 10,933 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 (10933 hom., cov: 31)
• Consequence: LOC105373779 XR_923656.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.200
• Publications: 0 publications found

Genes affected

LOC105373779 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.47 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105373779	XR_923656.1	n.233-1260G>A		intron_variant	Intron 2 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.348 AC: 52809 AN: 151774 Hom.: 10937 Cov.: 31

Gnomad AFR AF: 0.149

Gnomad AMI AF: 0.503

Gnomad AMR AF: 0.379

Gnomad ASJ AF: 0.459

Gnomad EAS AF: 0.0548

Gnomad SAS AF: 0.371

Gnomad FIN AF: 0.345

Gnomad MID AF: 0.484

Gnomad NFE AF: 0.474

Gnomad OTH AF: 0.384

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

GnomAD4 genome AF: 0.348 AC: 52804 AN: 151894 Hom.: 10933 Cov.: 31 AF XY: 0.342 AC XY: 25363 AN XY: 74244

African (AFR) AF: 0.148 AC: 6159 AN: 41486

American (AMR) AF: 0.379 AC: 5780 AN: 15244

Ashkenazi Jewish (ASJ) AF: 0.459 AC: 1591 AN: 3464

East Asian (EAS) AF: 0.0542 AC: 280 AN: 5168

South Asian (SAS) AF: 0.371 AC: 1784 AN: 4810

European-Finnish (FIN) AF: 0.345 AC: 3624 AN: 10492

Middle Eastern (MID) AF: 0.480 AC: 141 AN: 294

European-Non Finnish (NFE) AF: 0.474 AC: 32183 AN: 67918

Other (OTH) AF: 0.382 AC: 805 AN: 2110

Alfa AF: 0.403 Hom.: 1647

Bravo AF: 0.341

Asia WGS AF: 0.199 AC: 691 AN: 3454

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.23
DANN	Benign	0.13
PhyloP100		-0.20

Splicing

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

Other links and lift over

dbSNP: rs768352; hg19: chr2-185329691;