XR_007067071.1:n.472T>A

Variant names:

• chr19-383057-T-A
• rs11880212
• XR_007067071.1:n.472T>A

Variant summary

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

The XR_007067071.1(LOC124904606):​n.472T>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 0.39 in 152,010 control chromosomes in the GnomAD database, including 12,794 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 0.39 (12794 hom., cov: 32)
• Consequence: LOC124904606 XR_007067071.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.839
• Publications: 1 publications found

Genes affected

LOC124904606 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.587 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000662087.1. You can select a different transcript below to see updated ACMG assignments.

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
	ENSG00000286667	ENST00000662087.1		n.96+237T>A		intron	N/A
	ENSG00000286667	ENST00000797533.1		n.450-1544T>A		intron	N/A
	ENSG00000286667	ENST00000797534.1		n.386-3529T>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.389 AC: 59145 AN: 151890 Hom.: 12755 Cov.: 32

Gnomad AFR AF: 0.593

Gnomad AMI AF: 0.330

Gnomad AMR AF: 0.327

Gnomad ASJ AF: 0.321

Gnomad EAS AF: 0.197

Gnomad SAS AF: 0.349

Gnomad FIN AF: 0.370

Gnomad MID AF: 0.283

Gnomad NFE AF: 0.306

Gnomad OTH AF: 0.357

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

GnomAD4 genome AF: 0.390 AC: 59240 AN: 152010 Hom.: 12794 Cov.: 32 AF XY: 0.389 AC XY: 28939 AN XY: 74306

African (AFR) AF: 0.593 AC: 24574 AN: 41428

American (AMR) AF: 0.327 AC: 4998 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.321 AC: 1113 AN: 3470

East Asian (EAS) AF: 0.197 AC: 1018 AN: 5162

South Asian (SAS) AF: 0.349 AC: 1681 AN: 4814

European-Finnish (FIN) AF: 0.370 AC: 3911 AN: 10584

Middle Eastern (MID) AF: 0.293 AC: 86 AN: 294

European-Non Finnish (NFE) AF: 0.306 AC: 20814 AN: 67952

Other (OTH) AF: 0.353 AC: 745 AN: 2108

Alfa AF: 0.374 Hom.: 1421

Bravo AF: 0.393

Asia WGS AF: 0.288 AC: 1004 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	2.5
DANN	Benign	0.32
PhyloP100		-0.84

Splicing

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

Other links and lift over

dbSNP: rs11880212; hg19: chr19-383057;