16-11454429-T-G

Variant names:

• chr16-11454429-T-G
• rs6498196
• NM_001370704.1:c.4045+2430A>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001370704.1(LOC400499):​c.4045+2430A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.787 in 152,126 control chromosomes in the GnomAD database, including 47,150 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 0.79 (47150 hom., cov: 33)
• Consequence: LOC400499 NM_001370704.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0990
• Publications: 5 publications found

Genes affected

LOC400499 (HGNC:0):

LOC400499 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.805 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC400499	NM_001370704.1	c.4045+2430A>C		intron_variant	Intron 28 of 66	ENST00000696174.1	NP_001357633.1
LOC400499	NM_001395505.1	c.4045+2430A>C		intron_variant	Intron 28 of 65		NP_001382434.1
LOC400499	XM_047434105.1	c.4045+2430A>C		intron_variant	Intron 28 of 66		XP_047290061.1
LOC400499	XM_017023946.1	c.829+2430A>C		intron_variant	Intron 6 of 44		XP_016879435.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000188897	ENST00000696174.1	c.4045+2430A>C		intron_variant	Intron 28 of 66		NM_001370704.1	ENSP00000512464.1
ENSG00000188897	ENST00000598234.6	c.4045+2430A>C		intron_variant	Intron 28 of 65	5		ENSP00000470478.3
ENSG00000188897	ENST00000595170.1	n.*2113+2430A>C		intron_variant	Intron 16 of 22	2		ENSP00000471908.1
ENSG00000188897	ENST00000600877.1	n.281+2430A>C		intron_variant	Intron 1 of 1	3

Frequencies

GnomAD3 genomes AF: 0.787 AC: 119609 AN: 152008 Hom.: 47123 Cov.: 33

Gnomad AFR AF: 0.781

Gnomad AMI AF: 0.704

Gnomad AMR AF: 0.813

Gnomad ASJ AF: 0.752

Gnomad EAS AF: 0.717

Gnomad SAS AF: 0.827

Gnomad FIN AF: 0.768

Gnomad MID AF: 0.791

Gnomad NFE AF: 0.794

Gnomad OTH AF: 0.764

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

GnomAD4 genome AF: 0.787 AC: 119687 AN: 152126 Hom.: 47150 Cov.: 33 AF XY: 0.784 AC XY: 58275 AN XY: 74350

African (AFR) AF: 0.781 AC: 32387 AN: 41482

American (AMR) AF: 0.813 AC: 12424 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.752 AC: 2605 AN: 3464

East Asian (EAS) AF: 0.716 AC: 3709 AN: 5178

South Asian (SAS) AF: 0.826 AC: 3979 AN: 4816

European-Finnish (FIN) AF: 0.768 AC: 8114 AN: 10568

Middle Eastern (MID) AF: 0.786 AC: 231 AN: 294

European-Non Finnish (NFE) AF: 0.794 AC: 53990 AN: 68014

Other (OTH) AF: 0.760 AC: 1606 AN: 2112

Alfa AF: 0.791 Hom.: 182888

Bravo AF: 0.790

Asia WGS AF: 0.767 AC: 2670 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	1.6
DANN	Benign	0.66
PhyloP100		-0.099
Mutation Taster		=100/0	polymorphism (auto)

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: rs6498196; hg19: chr16-11548285;