16-11387988-A-T

Variant names:

• chr16-11387988-A-T
• rs4076823
• NM_001370704.1:c.9015-693T>A

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_001370704.1(LOC400499):​c.9015-693T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 31)
• Consequence: LOC400499 NM_001370704.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.414
• Publications: 3 publications found

Genes affected

LOC400499 (HGNC:0):

LOC400499 (HGNC:):

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC400499	NM_001370704.1	c.9015-693T>A		intron_variant	Intron 60 of 66	ENST00000696174.1	NP_001357633.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000188897	ENST00000696174.1	c.9015-693T>A		intron_variant	Intron 60 of 66		NM_001370704.1	ENSP00000512464.1
ENSG00000188897	ENST00000598234.6	c.8853-693T>A		intron_variant	Intron 59 of 65	5		ENSP00000470478.3
ENSG00000188897	ENST00000599216.5	c.417-693T>A		intron_variant	Intron 4 of 10	5		ENSP00000472859.1
ENSG00000188897	ENST00000600548.1	n.351-693T>A		intron_variant	Intron 1 of 1	3

Frequencies

GnomAD3 genomes Cov.: 31

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

GnomAD4 genome Cov.: 31

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.6
DANN	Benign	0.56
PhyloP100		-0.41

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

Other links and lift over

dbSNP: rs4076823; hg19: chr16-11481845;