6-16195077-T-C

Variant names:

• chr6-16195077-T-C
• rs2327951
• ENST00000755734.1:n.516+5518A>G

Variant summary

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

The ENST00000755734.1(ENSG00000298476):​n.516+5518A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.409 in 151,674 control chromosomes in the GnomAD database, including 15,251 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 0.41 (15251 hom., cov: 30)
• Consequence: ENSG00000298476 ENST00000755734.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0640
• Publications: 11 publications found

Genes affected

ENSG00000298476 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.721 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000298476	ENST00000755734.1	n.516+5518A>G		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.409 AC: 61976 AN: 151558 Hom.: 15208 Cov.: 30

Gnomad AFR AF: 0.671

Gnomad AMI AF: 0.308

Gnomad AMR AF: 0.367

Gnomad ASJ AF: 0.308

Gnomad EAS AF: 0.742

Gnomad SAS AF: 0.345

Gnomad FIN AF: 0.242

Gnomad MID AF: 0.226

Gnomad NFE AF: 0.274

Gnomad OTH AF: 0.358

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

GnomAD4 genome AF: 0.409 AC: 62076 AN: 151674 Hom.: 15251 Cov.: 30 AF XY: 0.406 AC XY: 30086 AN XY: 74132

African (AFR) AF: 0.671 AC: 27702 AN: 41256

American (AMR) AF: 0.367 AC: 5594 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.308 AC: 1069 AN: 3466

East Asian (EAS) AF: 0.741 AC: 3825 AN: 5162

South Asian (SAS) AF: 0.344 AC: 1653 AN: 4812

European-Finnish (FIN) AF: 0.242 AC: 2534 AN: 10484

Middle Eastern (MID) AF: 0.229 AC: 67 AN: 292

European-Non Finnish (NFE) AF: 0.274 AC: 18588 AN: 67936

Other (OTH) AF: 0.363 AC: 764 AN: 2106

Alfa AF: 0.285 Hom.: 3774

Bravo AF: 0.430

Asia WGS AF: 0.591 AC: 2053 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	4.5
DANN	Benign	0.73
PhyloP100		-0.064

Splicing

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

Other links and lift over

dbSNP: rs2327951; hg19: chr6-16195308;