chr4-28208406-T-C

Position:

• chr4-28208406-T-C

Variant summary

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

The XR_001741640.2(LOC105374557):​n.751-6663T>C 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 0.233 in 152,030 control chromosomes in the GnomAD database, including 5,298 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 0.23 (5298 hom., cov: 31)
• Consequence: LOC105374557 XR_001741640.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.13

Genes affected

LOC105374557 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.547 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105374557	XR_001741640.2	n.751-6663T>C		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.233 AC: 35379 AN: 151912 Hom.: 5289 Cov.: 31

Gnomad AFR AF: 0.0599

Gnomad AMI AF: 0.242

Gnomad AMR AF: 0.259

Gnomad ASJ AF: 0.264

Gnomad EAS AF: 0.564

Gnomad SAS AF: 0.391

Gnomad FIN AF: 0.397

Gnomad MID AF: 0.278

Gnomad NFE AF: 0.269

Gnomad OTH AF: 0.242

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

GnomAD4 genome AF: 0.233 AC: 35391 AN: 152030 Hom.: 5298 Cov.: 31 AF XY: 0.243 AC XY: 18086 AN XY: 74282

Gnomad4 AFR AF: 0.0597

Gnomad4 AMR AF: 0.259

Gnomad4 ASJ AF: 0.264

Gnomad4 EAS AF: 0.564

Gnomad4 SAS AF: 0.390

Gnomad4 FIN AF: 0.397

Gnomad4 NFE AF: 0.269

Gnomad4 OTH AF: 0.250

Alfa AF: 0.264 Hom.: 2592

Bravo AF: 0.214

Asia WGS AF: 0.487 AC: 1690 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	9.0
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: rs3925061; hg19: chr4-28210028;