rs1411374

Variant names:

• chr9-27713846-T-A
• rs1411374
• XM_047424284.1:c.80+2181T>A

Variant summary

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

The XR_007061442.1(LOC124902135):​n.139+2181T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.19 in 152,168 control chromosomes in the GnomAD database, including 3,135 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 0.19 (3135 hom., cov: 32)
• Consequence: LOC124902135 XR_007061442.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.839
• Publications: 2 publications found

Genes affected

LOC124902135 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.29 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.190 AC: 28895 AN: 152048 Hom.: 3131 Cov.: 32

Gnomad AFR AF: 0.112

Gnomad AMI AF: 0.222

Gnomad AMR AF: 0.297

Gnomad ASJ AF: 0.228

Gnomad EAS AF: 0.0503

Gnomad SAS AF: 0.276

Gnomad FIN AF: 0.198

Gnomad MID AF: 0.225

Gnomad NFE AF: 0.214

Gnomad OTH AF: 0.200

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

GnomAD4 genome AF: 0.190 AC: 28907 AN: 152168 Hom.: 3135 Cov.: 32 AF XY: 0.194 AC XY: 14450 AN XY: 74382

African (AFR) AF: 0.112 AC: 4651 AN: 41512

American (AMR) AF: 0.297 AC: 4537 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.228 AC: 791 AN: 3472

East Asian (EAS) AF: 0.0504 AC: 261 AN: 5178

South Asian (SAS) AF: 0.275 AC: 1330 AN: 4830

European-Finnish (FIN) AF: 0.198 AC: 2094 AN: 10590

Middle Eastern (MID) AF: 0.214 AC: 63 AN: 294

European-Non Finnish (NFE) AF: 0.214 AC: 14563 AN: 67982

Other (OTH) AF: 0.197 AC: 415 AN: 2110

Alfa AF: 0.199 Hom.: 402

Bravo AF: 0.194

Asia WGS AF: 0.164 AC: 569 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.81
DANN	Benign	0.71
PhyloP100		-0.84

Splicing

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

Other links and lift over

dbSNP: rs1411374; hg19: chr9-27713844;