4-180920041-C-T

Position:

• chr4-180920041-C-T

Variant summary

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

The XR_007058399.1(LOC124900821):​n.206-860G>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 0.903 in 151,986 control chromosomes in the GnomAD database, including 62,284 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 0.90 (62284 hom., cov: 34)
• Consequence: LOC124900821 XR_007058399.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.256

Genes affected

LOC124900821 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.974 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC124900821	XR_007058399.1	n.206-860G>A		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.903 AC: 137176 AN: 151870 Hom.: 62254 Cov.: 34

Gnomad AFR AF: 0.786

Gnomad AMI AF: 0.964

Gnomad AMR AF: 0.942

Gnomad ASJ AF: 0.976

Gnomad EAS AF: 0.996

Gnomad SAS AF: 0.971

Gnomad FIN AF: 0.966

Gnomad MID AF: 0.965

Gnomad NFE AF: 0.938

Gnomad OTH AF: 0.932

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

GnomAD4 genome AF: 0.903 AC: 137256 AN: 151986 Hom.: 62284 Cov.: 34 AF XY: 0.908 AC XY: 67458 AN XY: 74328

Gnomad4 AFR AF: 0.785

Gnomad4 AMR AF: 0.943

Gnomad4 ASJ AF: 0.976

Gnomad4 EAS AF: 0.996

Gnomad4 SAS AF: 0.971

Gnomad4 FIN AF: 0.966

Gnomad4 NFE AF: 0.938

Gnomad4 OTH AF: 0.932

Alfa AF: 0.915 Hom.: 3067

Bravo AF: 0.901

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	3.4
DANN	Benign	0.67

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1969398; hg19: chr4-181841194;