rs6498196

Positions:

• chr16-11454429-T-A
• chr16-11454429-T-G

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_001370704.1(LOC400499):​c.4045+2430A>T 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: 33)
• Consequence: LOC400499 NM_001370704.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0990

Genes affected

LOC400499 (HGNC:):

ACMG classification

Verdict is Likely_benign. Variant got -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC400499	NM_001370704.1	c.4045+2430A>T		intron_variant		ENST00000696174.1	NP_001357633.1
LOC400499	NM_001395505.1	c.4045+2430A>T		intron_variant			NP_001382434.1
LOC400499	XM_047434105.1	c.4045+2430A>T		intron_variant			XP_047290061.1
LOC400499	XM_017023946.1	c.829+2430A>T		intron_variant			XP_016879435.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000188897	ENST00000696174.1	c.4045+2430A>T		intron_variant			NM_001370704.1	ENSP00000512464.1
ENSG00000188897	ENST00000598234.6	c.4045+2430A>T		intron_variant		5		ENSP00000470478.3
ENSG00000188897	ENST00000595170.1	n.*2113+2430A>T		intron_variant		2		ENSP00000471908.1
ENSG00000188897	ENST00000600877.1	n.281+2430A>T		intron_variant		3

Frequencies

GnomAD3 genomes Cov.: 33

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

GnomAD4 genome Cov.: 33

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.5
DANN	Benign	0.54

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: rs6498196; hg19: chr16-11548285;