rs16880441

Positions:

• chr6-88266258-C-G

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000648572.1(ENSG00000234426):​n.990+14556G>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 0.0823 in 151,814 control chromosomes in the GnomAD database, including 552 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 0.082 (552 hom., cov: 32)
• Consequence: ENST00000648572.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.10

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.2).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.1 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000648572.1	n.990+14556G>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.0823 AC: 12481 AN: 151698 Hom.: 548 Cov.: 32

Gnomad AFR AF: 0.0764

Gnomad AMI AF: 0.0779

Gnomad AMR AF: 0.102

Gnomad ASJ AF: 0.0519

Gnomad EAS AF: 0.107

Gnomad SAS AF: 0.0727

Gnomad FIN AF: 0.120

Gnomad MID AF: 0.0728

Gnomad NFE AF: 0.0760

Gnomad OTH AF: 0.0817

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

GnomAD4 genome AF: 0.0823 AC: 12494 AN: 151814 Hom.: 552 Cov.: 32 AF XY: 0.0846 AC XY: 6275 AN XY: 74172

Gnomad4 AFR AF: 0.0762

Gnomad4 AMR AF: 0.102

Gnomad4 ASJ AF: 0.0519

Gnomad4 EAS AF: 0.107

Gnomad4 SAS AF: 0.0721

Gnomad4 FIN AF: 0.120

Gnomad4 NFE AF: 0.0760

Gnomad4 OTH AF: 0.0889

Alfa AF: 0.0828 Hom.: 363

Bravo AF: 0.0825

Asia WGS AF: 0.133 AC: 462 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.20
CADD	Benign	20
DANN	Benign	0.77

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs16880441; hg19: chr6-88975977;