chr4-54776950-G-A

Position:

• chr4-54776950-G-A

Variant summary

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

The XR_941056.3(LOC105377657):​n.1013+1262G>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 0.166 in 152,106 control chromosomes in the GnomAD database, including 2,266 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 0.17 (2266 hom., cov: 32)
• Consequence: LOC105377657 XR_941056.3 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.907

Genes affected

LOC105377657 (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 = 0.284 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105377657	XR_941056.3	n.1013+1262G>A		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.166 AC: 25214 AN: 151988 Hom.: 2265 Cov.: 32

Gnomad AFR AF: 0.152

Gnomad AMI AF: 0.160

Gnomad AMR AF: 0.118

Gnomad ASJ AF: 0.0897

Gnomad EAS AF: 0.296

Gnomad SAS AF: 0.234

Gnomad FIN AF: 0.207

Gnomad MID AF: 0.0696

Gnomad NFE AF: 0.169

Gnomad OTH AF: 0.141

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

GnomAD4 genome AF: 0.166 AC: 25214 AN: 152106 Hom.: 2266 Cov.: 32 AF XY: 0.168 AC XY: 12497 AN XY: 74350

Gnomad4 AFR AF: 0.152

Gnomad4 AMR AF: 0.118

Gnomad4 ASJ AF: 0.0897

Gnomad4 EAS AF: 0.296

Gnomad4 SAS AF: 0.234

Gnomad4 FIN AF: 0.207

Gnomad4 NFE AF: 0.169

Gnomad4 OTH AF: 0.142

Alfa AF: 0.159 Hom.: 4134

Bravo AF: 0.160

Asia WGS AF: 0.243 AC: 845 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	1.1
DANN	Benign	0.42

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11732323; hg19: chr4-55643116;