4-66868139-G-A

Position:

• chr4-66868139-G-A

Variant summary

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

The XR_938848.2(LOC105377262):​n.426+2627C>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 0.768 in 152,080 control chromosomes in the GnomAD database, including 45,975 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 0.77 (45975 hom., cov: 32)
• Consequence: LOC105377262 XR_938848.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.366

Genes affected

LOC105377262 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.69).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.877 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105377262	XR_938848.2	n.426+2627C>T		intron_variant, non_coding_transcript_variant
LOC105377262	XR_938847.2	n.509C>T		non_coding_transcript_exon_variant	3/4

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.768 AC: 116766 AN: 151962 Hom.: 45960 Cov.: 32

Gnomad AFR AF: 0.579

Gnomad AMI AF: 0.873

Gnomad AMR AF: 0.840

Gnomad ASJ AF: 0.866

Gnomad EAS AF: 0.899

Gnomad SAS AF: 0.701

Gnomad FIN AF: 0.841

Gnomad MID AF: 0.867

Gnomad NFE AF: 0.843

Gnomad OTH AF: 0.804

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

GnomAD4 genome AF: 0.768 AC: 116827 AN: 152080 Hom.: 45975 Cov.: 32 AF XY: 0.770 AC XY: 57232 AN XY: 74348

Gnomad4 AFR AF: 0.579

Gnomad4 AMR AF: 0.840

Gnomad4 ASJ AF: 0.866

Gnomad4 EAS AF: 0.899

Gnomad4 SAS AF: 0.702

Gnomad4 FIN AF: 0.841

Gnomad4 NFE AF: 0.843

Gnomad4 OTH AF: 0.804

Alfa AF: 0.835 Hom.: 123317

Bravo AF: 0.765

Asia WGS AF: 0.764 AC: 2655 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.69
CADD	Benign	7.4
DANN	Benign	0.72

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1155865; hg19: chr4-67733857;