rs16850918

Variant names:

• chr4-74319044-A-G
• rs16850918
• ENST00000805841.1:n.298+11154T>C

Variant summary

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

The ENST00000805841.1(ENSG00000304732):​n.298+11154T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0602 in 152,256 control chromosomes in the GnomAD database, including 632 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 0.060 (632 hom., cov: 32)
• Consequence: ENSG00000304732 ENST00000805841.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.369
• Publications: 2 publications found

Genes affected

ENSG00000304732 (HGNC:58817):

LOC105377276 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.157 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000805841.1. 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
	LOC105377276	NR_188415.1		n.298+11154T>C		intron	N/A
	LOC105377276	NR_188416.1		n.272+11154T>C		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000304732	ENST00000805841.1		n.298+11154T>C		intron	N/A
	ENSG00000304732	ENST00000805842.1		n.395+11154T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0600 AC: 9126 AN: 152138 Hom.: 629 Cov.: 32

Gnomad AFR AF: 0.160

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0510

Gnomad ASJ AF: 0.00375

Gnomad EAS AF: 0.0532

Gnomad SAS AF: 0.0768

Gnomad FIN AF: 0.00886

Gnomad MID AF: 0.0411

Gnomad NFE AF: 0.0122

Gnomad OTH AF: 0.0613

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

GnomAD4 genome AF: 0.0602 AC: 9164 AN: 152256 Hom.: 632 Cov.: 32 AF XY: 0.0604 AC XY: 4494 AN XY: 74458

African (AFR) AF: 0.160 AC: 6646 AN: 41504

American (AMR) AF: 0.0514 AC: 787 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.00375 AC: 13 AN: 3470

East Asian (EAS) AF: 0.0535 AC: 278 AN: 5192

South Asian (SAS) AF: 0.0775 AC: 374 AN: 4826

European-Finnish (FIN) AF: 0.00886 AC: 94 AN: 10614

Middle Eastern (MID) AF: 0.0442 AC: 13 AN: 294

European-Non Finnish (NFE) AF: 0.0122 AC: 829 AN: 68032

Other (OTH) AF: 0.0616 AC: 130 AN: 2110

Alfa AF: 0.0309 Hom.: 92

Bravo AF: 0.0673

Asia WGS AF: 0.0900 AC: 312 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	2.8
DANN	Benign	0.67
PhyloP100		0.37

Splicing

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

Other links and lift over

dbSNP: rs16850918; hg19: chr4-75184761;