rs4437278

chr4-12486575-G-A

Variant summary

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

The XR_001741374.1(LOC105374492):n.255-15845C>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 0.159 in 151,864 control chromosomes in the GnomAD database, including 2,194 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 0.16 (2194 hom., cov: 32)
• Consequence: LOC105374492 XR_001741374.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.352

Genes affected

LOC105374492 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.76).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.235 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105374492	XR_001741374.1	n.255-15845C>T		intron_variant, non_coding_transcript_variant
LOC105374492	XR_001741375.1	n.676-15845C>T		intron_variant, non_coding_transcript_variant
LOC105374492	XR_925406.4	n.478-15845C>T		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.159 AC: 24168 AN: 151746 Hom.: 2192 Cov.: 32

Gnomad AFR AF: 0.240

Gnomad AMI AF: 0.130

Gnomad AMR AF: 0.159

Gnomad ASJ AF: 0.152

Gnomad EAS AF: 0.128

Gnomad SAS AF: 0.106

Gnomad FIN AF: 0.0614

Gnomad MID AF: 0.282

Gnomad NFE AF: 0.131

Gnomad OTH AF: 0.205

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

GnomAD4 genome AF: 0.159 AC: 24191 AN: 151864 Hom.: 2194 Cov.: 32 AF XY: 0.155 AC XY: 11483 AN XY: 74200

Gnomad4 AFR AF: 0.239

Gnomad4 AMR AF: 0.159

Gnomad4 ASJ AF: 0.152

Gnomad4 EAS AF: 0.128

Gnomad4 SAS AF: 0.107

Gnomad4 FIN AF: 0.0614

Gnomad4 NFE AF: 0.131

Gnomad4 OTH AF: 0.207

Alfa AF: 0.138 Hom.: 895

Bravo AF: 0.172

Asia WGS AF: 0.160 AC: 556 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.76
Cadd	Benign	2.2
Dann	Benign	0.86

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4437278; hg19: chr4-12488199;