chr16-84121084-C-T

Variant names:

• chr16-84121084-C-T
• rs8045610
• ENST00000563242.2:n.952-6C>T

Variant summary

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

The ENST00000563242.2(ENSG00000260410):​n.952-6C>T variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.492 in 151,898 control chromosomes in the GnomAD database, including 18,508 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 0.49 (18503 hom., cov: 32)
  • Exomes 𝑓: 0.50 (5 hom.)
• Consequence: ENSG00000260410 ENST00000563242.2 splice_region, intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.281
• Publications: 8 publications found

Genes affected

ENSG00000260410 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.73).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.639 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000563242.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000260410	ENST00000563242.2	TSL:6	n.952-6C>T		splice_region intron	N/A

Frequencies

GnomAD3 genomes AF: 0.492 AC: 74681 AN: 151732 Hom.: 18481 Cov.: 32

Gnomad AFR AF: 0.491

Gnomad AMI AF: 0.566

Gnomad AMR AF: 0.526

Gnomad ASJ AF: 0.532

Gnomad EAS AF: 0.657

Gnomad SAS AF: 0.427

Gnomad FIN AF: 0.502

Gnomad MID AF: 0.551

Gnomad NFE AF: 0.472

Gnomad OTH AF: 0.514

GnomAD4 exome AF: 0.500 AC: 24 AN: 48 Hom.: 5 Cov.: 0 AF XY: 0.533 AC XY: 16 AN XY: 30

African (AFR) AF: 0.00 AC: 0 AN: 4

American (AMR) AF: 0.500 AC: 1 AN: 2

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.625 AC: 10 AN: 16

Middle Eastern (MID) AF: 0.500 AC: 1 AN: 2

European-Non Finnish (NFE) AF: 0.500 AC: 11 AN: 22

Other (OTH) AF: 0.500 AC: 1 AN: 2

GnomAD4 genome AF: 0.492 AC: 74750 AN: 151850 Hom.: 18503 Cov.: 32 AF XY: 0.494 AC XY: 36632 AN XY: 74186

African (AFR) AF: 0.490 AC: 20306 AN: 41400

American (AMR) AF: 0.527 AC: 8034 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.532 AC: 1828 AN: 3436

East Asian (EAS) AF: 0.658 AC: 3389 AN: 5152

South Asian (SAS) AF: 0.428 AC: 2061 AN: 4816

European-Finnish (FIN) AF: 0.502 AC: 5294 AN: 10536

Middle Eastern (MID) AF: 0.538 AC: 157 AN: 292

European-Non Finnish (NFE) AF: 0.472 AC: 32088 AN: 67948

Other (OTH) AF: 0.511 AC: 1078 AN: 2110

Alfa AF: 0.480 Hom.: 47996

Bravo AF: 0.497

Asia WGS AF: 0.516 AC: 1790 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.73
CADD	Benign	0.58
DANN	Benign	0.65
PhyloP100		0.28

Splicing

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

Other links and lift over

dbSNP: rs8045610; hg19: chr16-84154689; COSMIC: COSV54741172;