rs16989370

Variant names:

• chr20-40847942-C-T
• rs16989370
• ENST00000758964.1:n.86+18159G>A

Variant summary

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

The ENST00000758964.1(ENSG00000229771):​n.86+18159G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0305 in 152,232 control chromosomes in the GnomAD database, including 156 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 0.030 (156 hom., cov: 32)
• Consequence: ENSG00000229771 ENST00000758964.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.226
• Publications: 1 publications found

Genes affected

ENSG00000229771 (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 (EAS) allele frequency at 95% confidence interval = 0.188 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
ENSG00000229771	ENST00000758964.1	n.86+18159G>A		intron_variant	Intron 1 of 5

Frequencies

GnomAD3 genomes AF: 0.0305 AC: 4642 AN: 152114 Hom.: 157 Cov.: 32

Gnomad AFR AF: 0.0306

Gnomad AMI AF: 0.0493

Gnomad AMR AF: 0.0184

Gnomad ASJ AF: 0.0277

Gnomad EAS AF: 0.198

Gnomad SAS AF: 0.0166

Gnomad FIN AF: 0.0203

Gnomad MID AF: 0.0380

Gnomad NFE AF: 0.0228

Gnomad OTH AF: 0.0335

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

GnomAD4 genome AF: 0.0305 AC: 4641 AN: 152232 Hom.: 156 Cov.: 32 AF XY: 0.0306 AC XY: 2281 AN XY: 74446

African (AFR) AF: 0.0305 AC: 1267 AN: 41528

American (AMR) AF: 0.0184 AC: 281 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.0277 AC: 96 AN: 3470

East Asian (EAS) AF: 0.198 AC: 1024 AN: 5178

South Asian (SAS) AF: 0.0164 AC: 79 AN: 4818

European-Finnish (FIN) AF: 0.0203 AC: 216 AN: 10618

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

European-Non Finnish (NFE) AF: 0.0228 AC: 1550 AN: 68006

Other (OTH) AF: 0.0341 AC: 72 AN: 2114

Alfa AF: 0.0257 Hom.: 13

Bravo AF: 0.0318

Asia WGS AF: 0.0700 AC: 242 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	9.2
DANN	Benign	0.72
PhyloP100		0.23

Splicing

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

Other links and lift over

dbSNP: rs16989370; hg19: chr20-39476582;