16-49314843-C-T

Position:

• chr16-49314843-C-T

Variant summary

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

The ENST00000647485.1(ENSG00000279249):​n.565-15624C>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 0.0611 in 152,232 control chromosomes in the GnomAD database, including 281 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 0.061 (281 hom., cov: 32)
• Consequence: ENST00000647485.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.677

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0688 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105371243	XR_933533.3	n.88+1585G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000647485.1	n.565-15624C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.0610 AC: 9279 AN: 152116 Hom.: 282 Cov.: 32

Gnomad AFR AF: 0.0526

Gnomad AMI AF: 0.0197

Gnomad AMR AF: 0.0586

Gnomad ASJ AF: 0.0928

Gnomad EAS AF: 0.0276

Gnomad SAS AF: 0.0245

Gnomad FIN AF: 0.0591

Gnomad MID AF: 0.0759

Gnomad NFE AF: 0.0705

Gnomad OTH AF: 0.0751

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

GnomAD4 genome AF: 0.0611 AC: 9302 AN: 152232 Hom.: 281 Cov.: 32 AF XY: 0.0609 AC XY: 4531 AN XY: 74432

Gnomad4 AFR AF: 0.0532

Gnomad4 AMR AF: 0.0584

Gnomad4 ASJ AF: 0.0928

Gnomad4 EAS AF: 0.0276

Gnomad4 SAS AF: 0.0247

Gnomad4 FIN AF: 0.0591

Gnomad4 NFE AF: 0.0705

Gnomad4 OTH AF: 0.0739

Alfa AF: 0.0530 Hom.: 143

Bravo AF: 0.0620

Asia WGS AF: 0.0330 AC: 115 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.63
DANN	Benign	0.80

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs8055192; hg19: chr16-49348754;