4-27988301-T-A

Position:

• chr4-27988301-T-A

Variant summary

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

The XR_001741500.1(LOC105374552):​n.156-5188T>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 0.476 in 151,850 control chromosomes in the GnomAD database, including 18,633 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 0.48 (18633 hom., cov: 31)
• Consequence: LOC105374552 XR_001741500.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.463

Genes affected

LOC105374552 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.742 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105374552	XR_001741500.1	n.156-5188T>A		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.476 AC: 72231 AN: 151732 Hom.: 18619 Cov.: 31

Gnomad AFR AF: 0.288

Gnomad AMI AF: 0.281

Gnomad AMR AF: 0.609

Gnomad ASJ AF: 0.464

Gnomad EAS AF: 0.762

Gnomad SAS AF: 0.728

Gnomad FIN AF: 0.497

Gnomad MID AF: 0.497

Gnomad NFE AF: 0.521

Gnomad OTH AF: 0.489

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

GnomAD4 genome AF: 0.476 AC: 72276 AN: 151850 Hom.: 18633 Cov.: 31 AF XY: 0.487 AC XY: 36101 AN XY: 74198

Gnomad4 AFR AF: 0.288

Gnomad4 AMR AF: 0.610

Gnomad4 ASJ AF: 0.464

Gnomad4 EAS AF: 0.762

Gnomad4 SAS AF: 0.728

Gnomad4 FIN AF: 0.497

Gnomad4 NFE AF: 0.521

Gnomad4 OTH AF: 0.494

Alfa AF: 0.488 Hom.: 2326

Bravo AF: 0.473

Asia WGS AF: 0.728 AC: 2533 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	2.7
DANN	Benign	0.21

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9884781; hg19: chr4-27989923;