rs16843235

Variant names:

• chr1-198516564-A-T
• rs16843235
• ENST00000660823.1:n.327+2987T>A

Variant summary

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

The ENST00000660823.1(ENSG00000287989):​n.327+2987T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0971 in 152,176 control chromosomes in the GnomAD database, including 924 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 0.097 (924 hom., cov: 31)
• Consequence: ENSG00000287989 ENST00000660823.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.308
• Publications: 3 publications found

Genes affected

ENSG00000287989 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.168 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105371677	XR_922398.3	n.260+2987T>A		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000287989	ENST00000660823.1	n.327+2987T>A		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.0970 AC: 14748 AN: 152058 Hom.: 921 Cov.: 31

Gnomad AFR AF: 0.171

Gnomad AMI AF: 0.0307

Gnomad AMR AF: 0.0714

Gnomad ASJ AF: 0.105

Gnomad EAS AF: 0.00270

Gnomad SAS AF: 0.0362

Gnomad FIN AF: 0.105

Gnomad MID AF: 0.0696

Gnomad NFE AF: 0.0688

Gnomad OTH AF: 0.0839

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

GnomAD4 genome AF: 0.0971 AC: 14772 AN: 152176 Hom.: 924 Cov.: 31 AF XY: 0.0975 AC XY: 7256 AN XY: 74406

African (AFR) AF: 0.171 AC: 7109 AN: 41486

American (AMR) AF: 0.0712 AC: 1088 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.105 AC: 365 AN: 3470

East Asian (EAS) AF: 0.00270 AC: 14 AN: 5182

South Asian (SAS) AF: 0.0362 AC: 175 AN: 4828

European-Finnish (FIN) AF: 0.105 AC: 1117 AN: 10600

Middle Eastern (MID) AF: 0.0748 AC: 22 AN: 294

European-Non Finnish (NFE) AF: 0.0688 AC: 4679 AN: 68014

Other (OTH) AF: 0.0830 AC: 175 AN: 2108

Alfa AF: 0.0900 Hom.: 109

Bravo AF: 0.0967

Asia WGS AF: 0.0310 AC: 110 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	4.3
DANN	Benign	0.65
PhyloP100		-0.31

Splicing

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

Other links and lift over

dbSNP: rs16843235; hg19: chr1-198485694;