rs16962916

Positions:

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

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XR_007064997.1(LOC124903646):​n.234+1369T>G variant causes a intron, non coding transcript 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: LOC124903646 XR_007064997.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.592

Genes affected

LOC124903646 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt
LOC124903646	XR_007064997.1	n.234+1369T>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

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

Gnomad4 AFR AF: 0.398

Gnomad4 AMR AF: 0.292

Gnomad4 ASJ AF: 0.351

Gnomad4 EAS AF: 0.472

Gnomad4 SAS AF: 0.348

Gnomad4 FIN AF: 0.182

Gnomad4 NFE AF: 0.198

Gnomad4 OTH AF: 0.279

Alfa AF: 0.223 Hom.: 4024

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs16962916; hg19: chr16-13900333;