2-55843927-G-A

Variant names:

• chr2-55843927-G-A
• rs7571341
• XR_002959388.2:n.228+19335G>A

Variant summary

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

The XR_002959388.2(LOC112268416):​n.228+19335G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0653 in 152,004 control chromosomes in the GnomAD database, including 361 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 0.065 (361 hom., cov: 32)
• Consequence: LOC112268416 XR_002959388.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.04
• Publications: 4 publications found

Genes affected

LOC112268416 (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 (AFR) allele frequency at 95% confidence interval = 0.0703 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.0652 AC: 9910 AN: 151886 Hom.: 357 Cov.: 32

Gnomad AFR AF: 0.0724

Gnomad AMI AF: 0.0883

Gnomad AMR AF: 0.0616

Gnomad ASJ AF: 0.0773

Gnomad EAS AF: 0.0219

Gnomad SAS AF: 0.0428

Gnomad FIN AF: 0.0643

Gnomad MID AF: 0.0918

Gnomad NFE AF: 0.0651

Gnomad OTH AF: 0.0837

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

GnomAD4 genome AF: 0.0653 AC: 9933 AN: 152004 Hom.: 361 Cov.: 32 AF XY: 0.0655 AC XY: 4866 AN XY: 74290

African (AFR) AF: 0.0725 AC: 3006 AN: 41464

American (AMR) AF: 0.0614 AC: 937 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.0773 AC: 268 AN: 3466

East Asian (EAS) AF: 0.0219 AC: 113 AN: 5158

South Asian (SAS) AF: 0.0435 AC: 209 AN: 4806

European-Finnish (FIN) AF: 0.0643 AC: 680 AN: 10574

Middle Eastern (MID) AF: 0.0850 AC: 25 AN: 294

European-Non Finnish (NFE) AF: 0.0651 AC: 4425 AN: 67968

Other (OTH) AF: 0.0899 AC: 190 AN: 2114

Alfa AF: 0.0643 Hom.: 529

Bravo AF: 0.0658

Asia WGS AF: 0.0490 AC: 169 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.40
DANN	Benign	0.66
PhyloP100		-1.0

Splicing

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

Other links and lift over

dbSNP: rs7571341; hg19: chr2-56071062;