16-76069739-C-A

Position:

• chr16-76069739-C-A

Variant summary

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

The XR_933750.3(LOC105371349):​n.485-4513G>T 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 0.329 in 151,836 control chromosomes in the GnomAD database, including 10,018 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 0.33 (10018 hom., cov: 32)
• Consequence: LOC105371349 XR_933750.3 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.790

Genes affected

LOC105371349 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.56 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105371349	XR_933750.3	n.485-4513G>T		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.329 AC: 49936 AN: 151718 Hom.: 9986 Cov.: 32

Gnomad AFR AF: 0.566

Gnomad AMI AF: 0.248

Gnomad AMR AF: 0.211

Gnomad ASJ AF: 0.270

Gnomad EAS AF: 0.109

Gnomad SAS AF: 0.264

Gnomad FIN AF: 0.177

Gnomad MID AF: 0.341

Gnomad NFE AF: 0.262

Gnomad OTH AF: 0.306

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

GnomAD4 genome AF: 0.329 AC: 50012 AN: 151836 Hom.: 10018 Cov.: 32 AF XY: 0.321 AC XY: 23796 AN XY: 74210

Gnomad4 AFR AF: 0.566

Gnomad4 AMR AF: 0.210

Gnomad4 ASJ AF: 0.270

Gnomad4 EAS AF: 0.109

Gnomad4 SAS AF: 0.262

Gnomad4 FIN AF: 0.177

Gnomad4 NFE AF: 0.262

Gnomad4 OTH AF: 0.312

Alfa AF: 0.307 Hom.: 991

Bravo AF: 0.338

Asia WGS AF: 0.229 AC: 792 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.025
DANN	Benign	0.34

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs160948; hg19: chr16-76103637;