rs16880395

Positions:

• chr4-28238041-C-T

Variant summary

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

The ENST00000668598.1(ENSG00000286321):​n.92+11981C>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 0.226 in 151,818 control chromosomes in the GnomAD database, including 4,097 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 (4097 hom., cov: 32)
• Consequence: ENST00000668598.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.99

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.287 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105374557	XR_001741640.2	n.830+22893C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000668598.1	n.92+11981C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.226 AC: 34276 AN: 151700 Hom.: 4095 Cov.: 32

Gnomad AFR AF: 0.292

Gnomad AMI AF: 0.248

Gnomad AMR AF: 0.177

Gnomad ASJ AF: 0.176

Gnomad EAS AF: 0.0684

Gnomad SAS AF: 0.105

Gnomad FIN AF: 0.171

Gnomad MID AF: 0.199

Gnomad NFE AF: 0.229

Gnomad OTH AF: 0.219

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

GnomAD4 genome AF: 0.226 AC: 34299 AN: 151818 Hom.: 4097 Cov.: 32 AF XY: 0.220 AC XY: 16322 AN XY: 74202

Gnomad4 AFR AF: 0.292

Gnomad4 AMR AF: 0.177

Gnomad4 ASJ AF: 0.176

Gnomad4 EAS AF: 0.0686

Gnomad4 SAS AF: 0.105

Gnomad4 FIN AF: 0.171

Gnomad4 NFE AF: 0.229

Gnomad4 OTH AF: 0.216

Alfa AF: 0.218 Hom.: 653

Bravo AF: 0.230

Asia WGS AF: 0.0830 AC: 289 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	1.6
DANN	Benign	0.62

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs16880395; hg19: chr4-28239663;