rs4076823

Positions:

• chr16-11387988-A-G
• chr16-11387988-A-T

Variant summary

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

The NM_001370704.1(LOC400499):​c.9015-693T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.686 in 152,018 control chromosomes in the GnomAD database, including 38,612 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 0.69 (38612 hom., cov: 31)
• Consequence: LOC400499 NM_001370704.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.414

Genes affected

LOC400499 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.815 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC400499	NM_001370704.1	c.9015-693T>C		intron_variant		ENST00000696174.1	NP_001357633.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000188897	ENST00000696174.1	c.9015-693T>C		intron_variant			NM_001370704.1	ENSP00000512464.1
ENSG00000188897	ENST00000598234.6	c.8853-693T>C		intron_variant		5		ENSP00000470478.3
ENSG00000188897	ENST00000599216.5	c.417-693T>C		intron_variant		5		ENSP00000472859.1
ENSG00000188897	ENST00000600548.1	n.351-693T>C		intron_variant		3

Frequencies

GnomAD3 genomes AF: 0.686 AC: 104186 AN: 151900 Hom.: 38598 Cov.: 31

Gnomad AFR AF: 0.381

Gnomad AMI AF: 0.939

Gnomad AMR AF: 0.794

Gnomad ASJ AF: 0.806

Gnomad EAS AF: 0.663

Gnomad SAS AF: 0.634

Gnomad FIN AF: 0.821

Gnomad MID AF: 0.725

Gnomad NFE AF: 0.821

Gnomad OTH AF: 0.714

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

GnomAD4 genome AF: 0.686 AC: 104225 AN: 152018 Hom.: 38612 Cov.: 31 AF XY: 0.685 AC XY: 50902 AN XY: 74300

Gnomad4 AFR AF: 0.381

Gnomad4 AMR AF: 0.795

Gnomad4 ASJ AF: 0.806

Gnomad4 EAS AF: 0.662

Gnomad4 SAS AF: 0.634

Gnomad4 FIN AF: 0.821

Gnomad4 NFE AF: 0.821

Gnomad4 OTH AF: 0.714

Alfa AF: 0.797 Hom.: 100376

Bravo AF: 0.677

Asia WGS AF: 0.620 AC: 2155 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.8
DANN	Benign	0.60

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs4076823; hg19: chr16-11481845;