XR_944070.3:n.201-680T>C

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 XR_944070.3(LOC105370591):​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: LOC105370591 XR_944070.3 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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000809762.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000305248	ENST00000809762.1		n.201-680T>C		intron	N/A

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 v4.9

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;