rs4129434

Positions:

• chr1-208941027-C-T

Variant summary

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

The XR_001738442.2(LOC107985255):​n.496-118857G>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 0.325 in 152,090 control chromosomes in the GnomAD database, including 8,504 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 0.32 (8504 hom., cov: 32)
• Consequence: LOC107985255 XR_001738442.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.74

Genes affected

LOC107985255 (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 = 0.382 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC107985255	XR_001738442.2	n.496-118857G>A		intron_variant, non_coding_transcript_variant
LOC107985255	XR_001738441.2	n.496-118857G>A		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.325 AC: 49390 AN: 151972 Hom.: 8506 Cov.: 32

Gnomad AFR AF: 0.236

Gnomad AMI AF: 0.399

Gnomad AMR AF: 0.290

Gnomad ASJ AF: 0.451

Gnomad EAS AF: 0.229

Gnomad SAS AF: 0.284

Gnomad FIN AF: 0.341

Gnomad MID AF: 0.465

Gnomad NFE AF: 0.386

Gnomad OTH AF: 0.349

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

GnomAD4 genome AF: 0.325 AC: 49399 AN: 152090 Hom.: 8504 Cov.: 32 AF XY: 0.321 AC XY: 23841 AN XY: 74322

Gnomad4 AFR AF: 0.236

Gnomad4 AMR AF: 0.290

Gnomad4 ASJ AF: 0.451

Gnomad4 EAS AF: 0.228

Gnomad4 SAS AF: 0.282

Gnomad4 FIN AF: 0.341

Gnomad4 NFE AF: 0.386

Gnomad4 OTH AF: 0.347

Alfa AF: 0.379 Hom.: 14539

Bravo AF: 0.317

Asia WGS AF: 0.246 AC: 855 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	0.011
DANN	Benign	0.37

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4129434; hg19: chr1-209114372;