16-11454934-G-T

Variant names:

• chr16-11454934-G-T
• rs7197119
• NM_001370704.1:c.4045+1925C>A

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+1925C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.317 in 151,988 control chromosomes in the GnomAD database, including 8,098 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 0.32 (8098 hom., cov: 32)
• Consequence: LOC400499 NM_001370704.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00
• Publications: 0 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=-1.04).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.445 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC400499	NM_001370704.1	c.4045+1925C>A		intron_variant	Intron 28 of 66	ENST00000696174.1	NP_001357633.1
LOC400499	NM_001395505.1	c.4045+1925C>A		intron_variant	Intron 28 of 65		NP_001382434.1
LOC400499	XM_047434105.1	c.4045+1925C>A		intron_variant	Intron 28 of 66		XP_047290061.1
LOC400499	XM_017023946.1	c.829+1925C>A		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+1925C>A		intron_variant	Intron 28 of 66		NM_001370704.1	ENSP00000512464.1
ENSG00000188897	ENST00000598234.6	c.4045+1925C>A		intron_variant	Intron 28 of 65	5		ENSP00000470478.3
ENSG00000188897	ENST00000595170.1	n.*2113+1925C>A		intron_variant	Intron 16 of 22	2		ENSP00000471908.1
ENSG00000188897	ENST00000600877.1	n.281+1925C>A		intron_variant	Intron 1 of 1	3

Frequencies

GnomAD3 genomes AF: 0.317 AC: 48090 AN: 151870 Hom.: 8081 Cov.: 32

Gnomad AFR AF: 0.342

Gnomad AMI AF: 0.185

Gnomad AMR AF: 0.453

Gnomad ASJ AF: 0.247

Gnomad EAS AF: 0.433

Gnomad SAS AF: 0.349

Gnomad FIN AF: 0.330

Gnomad MID AF: 0.199

Gnomad NFE AF: 0.264

Gnomad OTH AF: 0.284

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

GnomAD4 genome AF: 0.317 AC: 48132 AN: 151988 Hom.: 8098 Cov.: 32 AF XY: 0.322 AC XY: 23914 AN XY: 74318

African (AFR) AF: 0.341 AC: 14145 AN: 41430

American (AMR) AF: 0.454 AC: 6934 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.247 AC: 856 AN: 3470

East Asian (EAS) AF: 0.433 AC: 2241 AN: 5172

South Asian (SAS) AF: 0.347 AC: 1669 AN: 4804

European-Finnish (FIN) AF: 0.330 AC: 3485 AN: 10554

Middle Eastern (MID) AF: 0.194 AC: 57 AN: 294

European-Non Finnish (NFE) AF: 0.265 AC: 17979 AN: 67966

Other (OTH) AF: 0.283 AC: 598 AN: 2114

Alfa AF: 0.258 Hom.: 3074

Bravo AF: 0.328

Asia WGS AF: 0.347 AC: 1210 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	1.3
DANN	Benign	0.73
PhyloP100		0.0
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: rs7197119; hg19: chr16-11548790;