XR_007062868.1:n.1840-221A>T

Variant names:

• chr11-102855411-A-T
• rs737693
• XR_007062868.1:n.1840-221A>T

Variant summary

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

The XR_007062868.1(LOC124902741):​n.1840-221A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0932 in 152,188 control chromosomes in the GnomAD database, including 943 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 0.093 (943 hom., cov: 32)
• Consequence: LOC124902741 XR_007062868.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.130
• Publications: 13 publications found

Genes affected

LOC124902741 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.127 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: 0.0933 AC: 14188 AN: 152070 Hom.: 942 Cov.: 32

Gnomad AFR AF: 0.0227

Gnomad AMI AF: 0.107

Gnomad AMR AF: 0.0710

Gnomad ASJ AF: 0.111

Gnomad EAS AF: 0.0260

Gnomad SAS AF: 0.0733

Gnomad FIN AF: 0.206

Gnomad MID AF: 0.130

Gnomad NFE AF: 0.129

Gnomad OTH AF: 0.0918

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

GnomAD4 genome AF: 0.0932 AC: 14190 AN: 152188 Hom.: 943 Cov.: 32 AF XY: 0.0947 AC XY: 7048 AN XY: 74396

African (AFR) AF: 0.0226 AC: 939 AN: 41564

American (AMR) AF: 0.0710 AC: 1085 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.111 AC: 385 AN: 3464

East Asian (EAS) AF: 0.0260 AC: 135 AN: 5186

South Asian (SAS) AF: 0.0740 AC: 356 AN: 4812

European-Finnish (FIN) AF: 0.206 AC: 2180 AN: 10564

Middle Eastern (MID) AF: 0.136 AC: 40 AN: 294

European-Non Finnish (NFE) AF: 0.129 AC: 8783 AN: 68000

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

Alfa AF: 0.115 Hom.: 144

Bravo AF: 0.0798

Asia WGS AF: 0.0540 AC: 188 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	8.5
DANN	Benign	0.74
PhyloP100		-0.13

Splicing

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

Other links and lift over

dbSNP: rs737693; hg19: chr11-102726142;