rs1431005

Positions:

• chr4-187424214-G-A
• chr4-187424214-G-C
• chr4-187424214-G-T

Variant summary

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

The NR_038931.1(LOC339975):​n.322+81078C>T 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 0.389 in 151,866 control chromosomes in the GnomAD database, including 11,671 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 (11671 hom., cov: 32)
• Consequence: LOC339975 NR_038931.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.431

Genes affected

LOC339975 (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 (NFE) allele frequency at 95% confidence interval = 0.401 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC339975	NR_038931.1	n.322+81078C>T		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.389 AC: 59097 AN: 151748 Hom.: 11662 Cov.: 32

Gnomad AFR AF: 0.365

Gnomad AMI AF: 0.305

Gnomad AMR AF: 0.337

Gnomad ASJ AF: 0.383

Gnomad EAS AF: 0.377

Gnomad SAS AF: 0.383

Gnomad FIN AF: 0.474

Gnomad MID AF: 0.418

Gnomad NFE AF: 0.405

Gnomad OTH AF: 0.396

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

GnomAD4 genome AF: 0.389 AC: 59125 AN: 151866 Hom.: 11671 Cov.: 32 AF XY: 0.390 AC XY: 28921 AN XY: 74208

Gnomad4 AFR AF: 0.365

Gnomad4 AMR AF: 0.337

Gnomad4 ASJ AF: 0.383

Gnomad4 EAS AF: 0.378

Gnomad4 SAS AF: 0.383

Gnomad4 FIN AF: 0.474

Gnomad4 NFE AF: 0.405

Gnomad4 OTH AF: 0.392

Alfa AF: 0.395 Hom.: 22777

Bravo AF: 0.377

Asia WGS AF: 0.370 AC: 1286 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	0.48
DANN	Benign	0.62

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1431005; hg19: chr4-188345368;