rs9919906

Variant names:

• chr14-80152832-T-C
• rs9919906
• ENST00000809762.1:n.201-680T>C

Variant summary

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

The ENST00000809762.1(ENSG00000305248):​n.201-680T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.513 in 151,226 control chromosomes in the GnomAD database, including 20,423 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 0.51 (20423 hom., cov: 31)
• Consequence: ENSG00000305248 ENST00000809762.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.860
• Publications: 1 publications found

Genes affected

ENSG00000305248 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.555 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105370591	XR_944070.3	n.201-680T>C		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000305248	ENST00000809762.1	n.201-680T>C		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.513 AC: 77545 AN: 151108 Hom.: 20400 Cov.: 31

Gnomad AFR AF: 0.458

Gnomad AMI AF: 0.579

Gnomad AMR AF: 0.475

Gnomad ASJ AF: 0.500

Gnomad EAS AF: 0.293

Gnomad SAS AF: 0.450

Gnomad FIN AF: 0.617

Gnomad MID AF: 0.592

Gnomad NFE AF: 0.560

Gnomad OTH AF: 0.519

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

GnomAD4 genome AF: 0.513 AC: 77604 AN: 151226 Hom.: 20423 Cov.: 31 AF XY: 0.513 AC XY: 37883 AN XY: 73854

African (AFR) AF: 0.459 AC: 18985 AN: 41404

American (AMR) AF: 0.474 AC: 7162 AN: 15118

Ashkenazi Jewish (ASJ) AF: 0.500 AC: 1726 AN: 3454

East Asian (EAS) AF: 0.293 AC: 1510 AN: 5150

South Asian (SAS) AF: 0.450 AC: 2164 AN: 4810

European-Finnish (FIN) AF: 0.617 AC: 6500 AN: 10528

Middle Eastern (MID) AF: 0.582 AC: 170 AN: 292

European-Non Finnish (NFE) AF: 0.560 AC: 37774 AN: 67462

Other (OTH) AF: 0.518 AC: 1086 AN: 2098

Alfa AF: 0.546 Hom.: 3273

Bravo AF: 0.498

Asia WGS AF: 0.348 AC: 1209 AN: 3466

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	1.2
DANN	Benign	0.47
PhyloP100		-0.86

Splicing

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

Other links and lift over

dbSNP: rs9919906; hg19: chr14-80619175;