rs1411374

Positions:

• chr9-27713846-T-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XR_007061442.1(LOC124902135):​n.139+2181T>A variant causes a intron, non coding transcript 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, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.839

Genes affected

LOC124902135 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC124902135	XR_007061442.1	n.139+2181T>A		intron_variant, non_coding_transcript_variant
LOC124902135	XM_047424284.1	c.80+2181T>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

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

Gnomad4 AFR AF: 0.112

Gnomad4 AMR AF: 0.297

Gnomad4 ASJ AF: 0.228

Gnomad4 EAS AF: 0.0504

Gnomad4 SAS AF: 0.275

Gnomad4 FIN AF: 0.198

Gnomad4 NFE AF: 0.214

Gnomad4 OTH AF: 0.197

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 v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1411374; hg19: chr9-27713844;