rs16873377

Variant names:

• chr4-23238968-C-T
• rs16873377
• ENST00000512563.1:n.138-3910G>A

Variant summary

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

The ENST00000512563.1(ENSG00000249547):​n.138-3910G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.133 in 152,038 control chromosomes in the GnomAD database, including 4,438 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 0.13 (4438 hom., cov: 32)
• Consequence: ENSG00000249547 ENST00000512563.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.05
• Publications: 0 publications found

Genes affected

ENSG00000249547 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.451 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000512563.1. 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
	ENSG00000249547	ENST00000512563.1	TSL:4	n.138-3910G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.133 AC: 20134 AN: 151920 Hom.: 4419 Cov.: 32

Gnomad AFR AF: 0.456

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0529

Gnomad ASJ AF: 0.00115

Gnomad EAS AF: 0.000386

Gnomad SAS AF: 0.00187

Gnomad FIN AF: 0.000283

Gnomad MID AF: 0.0348

Gnomad NFE AF: 0.00360

Gnomad OTH AF: 0.0981

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

GnomAD4 genome AF: 0.133 AC: 20192 AN: 152038 Hom.: 4438 Cov.: 32 AF XY: 0.129 AC XY: 9579 AN XY: 74328

African (AFR) AF: 0.457 AC: 18908 AN: 41418

American (AMR) AF: 0.0527 AC: 806 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.00115 AC: 4 AN: 3466

East Asian (EAS) AF: 0.000386 AC: 2 AN: 5176

South Asian (SAS) AF: 0.00187 AC: 9 AN: 4818

European-Finnish (FIN) AF: 0.000283 AC: 3 AN: 10588

Middle Eastern (MID) AF: 0.0374 AC: 11 AN: 294

European-Non Finnish (NFE) AF: 0.00359 AC: 244 AN: 67974

Other (OTH) AF: 0.0971 AC: 205 AN: 2112

Alfa AF: 0.0788 Hom.: 309

Bravo AF: 0.150

Asia WGS AF: 0.0300 AC: 106 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.10
DANN	Benign	0.53
PhyloP100		-2.0

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs16873377;

hg19: chr4-23240591;