6-16113502-C-T

Variant names:

• chr6-16113502-C-T
• rs2480
• ENST00000806821.1:n.590-7912C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000806821.1(ENSG00000289953):​n.590-7912C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.604 in 152,042 control chromosomes in the GnomAD database, including 30,096 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 0.60 (30096 hom., cov: 32)
• Consequence: ENSG00000289953 ENST00000806821.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.147
• Publications: 10 publications found

Genes affected

ENSG00000289953 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.863 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000806821.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000289953	ENST00000806821.1		n.590-7912C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.603 AC: 91643 AN: 151924 Hom.: 30035 Cov.: 32

Gnomad AFR AF: 0.871

Gnomad AMI AF: 0.448

Gnomad AMR AF: 0.595

Gnomad ASJ AF: 0.550

Gnomad EAS AF: 0.694

Gnomad SAS AF: 0.590

Gnomad FIN AF: 0.432

Gnomad MID AF: 0.487

Gnomad NFE AF: 0.469

Gnomad OTH AF: 0.565

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

GnomAD4 genome AF: 0.604 AC: 91762 AN: 152042 Hom.: 30096 Cov.: 32 AF XY: 0.599 AC XY: 44528 AN XY: 74320

African (AFR) AF: 0.871 AC: 36172 AN: 41536

American (AMR) AF: 0.595 AC: 9093 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.550 AC: 1908 AN: 3470

East Asian (EAS) AF: 0.694 AC: 3586 AN: 5168

South Asian (SAS) AF: 0.590 AC: 2845 AN: 4826

European-Finnish (FIN) AF: 0.432 AC: 4547 AN: 10534

Middle Eastern (MID) AF: 0.486 AC: 143 AN: 294

European-Non Finnish (NFE) AF: 0.469 AC: 31863 AN: 67924

Other (OTH) AF: 0.569 AC: 1197 AN: 2104

Alfa AF: 0.516 Hom.: 82440

Bravo AF: 0.631

Asia WGS AF: 0.665 AC: 2312 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	1.9
DANN	Benign	0.54
PhyloP100		0.15

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs2480;

hg19: chr6-16113733;