chr4-180916588-C-T

Position:

• chr4-180916588-C-T

Variant summary

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

The XR_001741481.2(LOC105377568):​n.163+1197G>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 0.901 in 152,118 control chromosomes in the GnomAD database, including 62,107 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 (62107 hom., cov: 31)
• Consequence: LOC105377568 XR_001741481.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.99

Genes affected

LOC105377568 (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 = 0.974 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105377568	XR_001741481.2	n.163+1197G>A		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.901 AC: 136935 AN: 152000 Hom.: 62077 Cov.: 31

Gnomad AFR AF: 0.779

Gnomad AMI AF: 0.964

Gnomad AMR AF: 0.944

Gnomad ASJ AF: 0.976

Gnomad EAS AF: 0.996

Gnomad SAS AF: 0.971

Gnomad FIN AF: 0.965

Gnomad MID AF: 0.965

Gnomad NFE AF: 0.937

Gnomad OTH AF: 0.932

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

GnomAD4 genome AF: 0.901 AC: 137013 AN: 152118 Hom.: 62107 Cov.: 31 AF XY: 0.905 AC XY: 67305 AN XY: 74362

Gnomad4 AFR AF: 0.778

Gnomad4 AMR AF: 0.944

Gnomad4 ASJ AF: 0.976

Gnomad4 EAS AF: 0.996

Gnomad4 SAS AF: 0.971

Gnomad4 FIN AF: 0.965

Gnomad4 NFE AF: 0.937

Gnomad4 OTH AF: 0.932

Alfa AF: 0.909 Hom.: 3049

Bravo AF: 0.896

Asia WGS AF: 0.947 AC: 3296 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	0.026
DANN	Benign	0.54

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6848893; hg19: chr4-181837741;