chr16-82626550-G-T

Variant names:

• chr16-82626550-G-T
• rs12444338
• ENST00000793365.1:n.760C>A

Variant summary

Our verdict is Benign. The variant received -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The ENST00000793365.1(ENSG00000303284):​n.760C>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.43 in 151,526 control chromosomes in the GnomAD database, including 14,610 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.43 (14610 hom., cov: 32)
• Consequence: ENSG00000303284 ENST00000793365.1 non_coding_transcript_exon
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.134
• Publications: 15 publications found

Genes affected

ENSG00000303284 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BP6: Variant 16-82626550-G-T is Benign according to our data. Variant chr16-82626550-G-T is described in ClinVar as Benign. ClinVar VariationId is 1241381.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.487 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000793365.1. 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
	ENSG00000303284	ENST00000793365.1		n.760C>A		non_coding_transcript_exon	Exon 1 of 2

Frequencies

GnomAD3 genomes AF: 0.431 AC: 65202 AN: 151408 Hom.: 14609 Cov.: 32

Gnomad AFR AF: 0.341

Gnomad AMI AF: 0.540

Gnomad AMR AF: 0.334

Gnomad ASJ AF: 0.425

Gnomad EAS AF: 0.331

Gnomad SAS AF: 0.450

Gnomad FIN AF: 0.567

Gnomad MID AF: 0.380

Gnomad NFE AF: 0.492

Gnomad OTH AF: 0.405

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

GnomAD4 genome AF: 0.430 AC: 65231 AN: 151526 Hom.: 14610 Cov.: 32 AF XY: 0.433 AC XY: 32014 AN XY: 73962

African (AFR) AF: 0.341 AC: 14090 AN: 41298

American (AMR) AF: 0.333 AC: 5087 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.425 AC: 1476 AN: 3470

East Asian (EAS) AF: 0.330 AC: 1696 AN: 5140

South Asian (SAS) AF: 0.448 AC: 2151 AN: 4798

European-Finnish (FIN) AF: 0.567 AC: 5924 AN: 10442

Middle Eastern (MID) AF: 0.388 AC: 114 AN: 294

European-Non Finnish (NFE) AF: 0.492 AC: 33352 AN: 67818

Other (OTH) AF: 0.406 AC: 853 AN: 2100

Alfa AF: 0.301 Hom.: 719

Bravo AF: 0.405

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Jun 18, 2021

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This variant is associated with the following publications: (PMID: 20887962)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.17
DANN	Benign	0.49
PhyloP100		-0.13
PromoterAI		-0.040	Neutral

Splicing

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

Other links and lift over

dbSNP: rs12444338; hg19: chr16-82660155;