16-77057714-C-T

Variant names:

• chr16-77057714-C-T
• rs9928199
• ENST00000805261.1:n.306-31577G>A

Variant summary

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

The ENST00000805261.1(ENSG00000304662):​n.306-31577G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.103 in 145,186 control chromosomes in the GnomAD database, including 2,489 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 0.10 (2489 hom., cov: 29)
• Consequence: ENSG00000304662 ENST00000805261.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0760
• Publications: 2 publications found

Genes affected

ENSG00000304662 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.155 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
ENSG00000304662	ENST00000805261.1	n.306-31577G>A		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.103 AC: 14966 AN: 145064 Hom.: 2478 Cov.: 29

Gnomad AFR AF: 0.158

Gnomad AMI AF: 0.118

Gnomad AMR AF: 0.0739

Gnomad ASJ AF: 0.0388

Gnomad EAS AF: 0.00219

Gnomad SAS AF: 0.120

Gnomad FIN AF: 0.105

Gnomad MID AF: 0.109

Gnomad NFE AF: 0.0846

Gnomad OTH AF: 0.0979

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

GnomAD4 genome AF: 0.103 AC: 14996 AN: 145186 Hom.: 2489 Cov.: 29 AF XY: 0.103 AC XY: 7284 AN XY: 70680

African (AFR) AF: 0.159 AC: 6446 AN: 40634

American (AMR) AF: 0.0738 AC: 1072 AN: 14526

Ashkenazi Jewish (ASJ) AF: 0.0388 AC: 127 AN: 3272

East Asian (EAS) AF: 0.00219 AC: 11 AN: 5018

South Asian (SAS) AF: 0.121 AC: 534 AN: 4424

European-Finnish (FIN) AF: 0.105 AC: 1026 AN: 9734

Middle Eastern (MID) AF: 0.110 AC: 29 AN: 264

European-Non Finnish (NFE) AF: 0.0846 AC: 5453 AN: 64426

Other (OTH) AF: 0.0968 AC: 194 AN: 2004

Alfa AF: 0.0929 Hom.: 1989

Asia WGS AF: 0.0820 AC: 280 AN: 3382

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	6.6
DANN	Benign	0.27
PhyloP100		0.076

Splicing

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

Other links and lift over

dbSNP: rs9928199; hg19: chr16-77091611;