rs1879908

Positions:

• chr4-180920703-C-A
• chr4-180920703-C-G

Variant summary

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

The XR_007058399.1(LOC124900821):​n.205+933G>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 0.889 in 152,202 control chromosomes in the GnomAD database, including 60,767 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 0.89 (60767 hom., cov: 32)
• Consequence: LOC124900821 XR_007058399.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.05

Genes affected

LOC124900821 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.973 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC124900821	XR_007058399.1	n.205+933G>T		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.890 AC: 135304 AN: 152084 Hom.: 60738 Cov.: 32

Gnomad AFR AF: 0.748

Gnomad AMI AF: 0.964

Gnomad AMR AF: 0.936

Gnomad ASJ AF: 0.974

Gnomad EAS AF: 0.996

Gnomad SAS AF: 0.967

Gnomad FIN AF: 0.962

Gnomad MID AF: 0.962

Gnomad NFE AF: 0.934

Gnomad OTH AF: 0.925

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

GnomAD4 genome AF: 0.889 AC: 135381 AN: 152202 Hom.: 60767 Cov.: 32 AF XY: 0.895 AC XY: 66564 AN XY: 74410

Gnomad4 AFR AF: 0.747

Gnomad4 AMR AF: 0.936

Gnomad4 ASJ AF: 0.974

Gnomad4 EAS AF: 0.996

Gnomad4 SAS AF: 0.968

Gnomad4 FIN AF: 0.962

Gnomad4 NFE AF: 0.934

Gnomad4 OTH AF: 0.925

Alfa AF: 0.905 Hom.: 7767

Bravo AF: 0.884

Asia WGS AF: 0.948 AC: 3297 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.15
DANN	Benign	0.47

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1879908; hg19: chr4-181841856;