rs16962916

Variant names:

• chr16-13806476-A-C
• rs16962916
• ENST00000761632.1:n.241+1369T>G

Your query was ambiguous. Multiple possible variants found:

• chr16-13806476-A-C
• chr16-13806476-A-G

Variant summary

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

The ENST00000761632.1(ENSG00000299216):​n.241+1369T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.279 in 152,152 control chromosomes in the GnomAD database, including 6,772 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 0.28 (6772 hom., cov: 33)
• Consequence: ENSG00000299216 ENST00000761632.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.592
• Publications: 3 publications found

Genes affected

ENSG00000299216 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.456 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124903646	XR_007064997.1	n.234+1369T>G		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000299216	ENST00000761632.1	n.241+1369T>G		intron_variant	Intron 1 of 1
ENSG00000299216	ENST00000761633.1	n.119+1485T>G		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.279 AC: 42465 AN: 152034 Hom.: 6761 Cov.: 33

Gnomad AFR AF: 0.397

Gnomad AMI AF: 0.134

Gnomad AMR AF: 0.292

Gnomad ASJ AF: 0.351

Gnomad EAS AF: 0.473

Gnomad SAS AF: 0.349

Gnomad FIN AF: 0.182

Gnomad MID AF: 0.310

Gnomad NFE AF: 0.198

Gnomad OTH AF: 0.278

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

GnomAD4 genome AF: 0.279 AC: 42520 AN: 152152 Hom.: 6772 Cov.: 33 AF XY: 0.283 AC XY: 21088 AN XY: 74402

African (AFR) AF: 0.398 AC: 16489 AN: 41460

American (AMR) AF: 0.292 AC: 4457 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.351 AC: 1215 AN: 3466

East Asian (EAS) AF: 0.472 AC: 2444 AN: 5180

South Asian (SAS) AF: 0.348 AC: 1681 AN: 4826

European-Finnish (FIN) AF: 0.182 AC: 1934 AN: 10604

Middle Eastern (MID) AF: 0.316 AC: 93 AN: 294

European-Non Finnish (NFE) AF: 0.198 AC: 13495 AN: 68010

Other (OTH) AF: 0.279 AC: 590 AN: 2114

Alfa AF: 0.243 Hom.: 7000

Bravo AF: 0.301

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.14
DANN	Benign	0.73
PhyloP100		-0.59

Splicing

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

Other links and lift over

dbSNP: rs16962916; hg19: chr16-13900333;