rs1390096

Positions:

• chr4-11501980-G-A

Variant summary

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

The XR_001741361.2(LOC107986178):​n.1666+19134G>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 0.228 in 151,996 control chromosomes in the GnomAD database, including 4,788 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 0.23 (4788 hom., cov: 32)
• Consequence: LOC107986178 XR_001741361.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.25

Genes affected

LOC107986178 (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 (EAS) allele frequency at 95% confidence interval = 0.457 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC107986178	XR_001741361.2	n.1666+19134G>A		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.228 AC: 34650 AN: 151878 Hom.: 4779 Cov.: 32

Gnomad AFR AF: 0.0828

Gnomad AMI AF: 0.301

Gnomad AMR AF: 0.231

Gnomad ASJ AF: 0.206

Gnomad EAS AF: 0.473

Gnomad SAS AF: 0.312

Gnomad FIN AF: 0.346

Gnomad MID AF: 0.177

Gnomad NFE AF: 0.274

Gnomad OTH AF: 0.222

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

GnomAD4 genome AF: 0.228 AC: 34665 AN: 151996 Hom.: 4788 Cov.: 32 AF XY: 0.235 AC XY: 17484 AN XY: 74264

Gnomad4 AFR AF: 0.0826

Gnomad4 AMR AF: 0.232

Gnomad4 ASJ AF: 0.206

Gnomad4 EAS AF: 0.473

Gnomad4 SAS AF: 0.313

Gnomad4 FIN AF: 0.346

Gnomad4 NFE AF: 0.274

Gnomad4 OTH AF: 0.225

Alfa AF: 0.267 Hom.: 6874

Bravo AF: 0.213

Asia WGS AF: 0.383 AC: 1330 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.029
DANN	Benign	0.31

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1390096; hg19: chr4-11503604;