rs16899168

Variant names:

• chr6-31290910-G-A
• rs16899168
• ENST00000755297.1:n.32+19804G>A

Variant summary

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

The ENST00000755297.1(ENSG00000298396):​n.32+19804G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0485 in 152,162 control chromosomes in the GnomAD database, including 298 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 0.049 (298 hom., cov: 32)
• Consequence: ENSG00000298396 ENST00000755297.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.64
• Publications: 7 publications found

Genes affected

ENSG00000298396 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.144 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000755297.1. 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
	ENSG00000298396	ENST00000755297.1		n.32+19804G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0485 AC: 7376 AN: 152044 Hom.: 295 Cov.: 32

Gnomad AFR AF: 0.0378

Gnomad AMI AF: 0.00549

Gnomad AMR AF: 0.113

Gnomad ASJ AF: 0.0271

Gnomad EAS AF: 0.132

Gnomad SAS AF: 0.154

Gnomad FIN AF: 0.0472

Gnomad MID AF: 0.0823

Gnomad NFE AF: 0.0285

Gnomad OTH AF: 0.0507

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

GnomAD4 genome AF: 0.0485 AC: 7380 AN: 152162 Hom.: 298 Cov.: 32 AF XY: 0.0532 AC XY: 3960 AN XY: 74370

African (AFR) AF: 0.0376 AC: 1562 AN: 41518

American (AMR) AF: 0.113 AC: 1730 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.0271 AC: 94 AN: 3468

East Asian (EAS) AF: 0.132 AC: 686 AN: 5180

South Asian (SAS) AF: 0.153 AC: 736 AN: 4808

European-Finnish (FIN) AF: 0.0472 AC: 499 AN: 10574

Middle Eastern (MID) AF: 0.0884 AC: 26 AN: 294

European-Non Finnish (NFE) AF: 0.0285 AC: 1935 AN: 68010

Other (OTH) AF: 0.0507 AC: 107 AN: 2112

Alfa AF: 0.0380 Hom.: 388

Bravo AF: 0.0521

Asia WGS AF: 0.153 AC: 530 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.083
DANN	Benign	0.55
PhyloP100		-2.6

Splicing

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

Other links and lift over

dbSNP: rs16899168; hg19: chr6-31258687;