4-16478734-G-A

Variant names:

• chr4-16478734-G-A
• rs6816070
• ENST00000512370.5:n.181-33199G>A

Variant summary

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

The ENST00000512370.5(ENSG00000248138):​n.181-33199G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.637 in 152,032 control chromosomes in the GnomAD database, including 31,627 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 0.64 (31627 hom., cov: 33)
• Consequence: ENSG00000248138 ENST00000512370.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.330
• Publications: 3 publications found

Genes affected

ENSG00000248138 (HGNC:58741):

LOC105374505 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.783 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000512370.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000248138	ENST00000512370.5	TSL:2	n.181-33199G>A		intron	N/A
	ENSG00000248138	ENST00000782749.1		n.223+52294G>A		intron	N/A
	ENSG00000248138	ENST00000782750.1		n.340+52294G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.638 AC: 96848 AN: 151914 Hom.: 31610 Cov.: 33

Gnomad AFR AF: 0.791

Gnomad AMI AF: 0.639

Gnomad AMR AF: 0.576

Gnomad ASJ AF: 0.659

Gnomad EAS AF: 0.462

Gnomad SAS AF: 0.512

Gnomad FIN AF: 0.536

Gnomad MID AF: 0.604

Gnomad NFE AF: 0.595

Gnomad OTH AF: 0.637

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

GnomAD4 genome AF: 0.637 AC: 96917 AN: 152032 Hom.: 31627 Cov.: 33 AF XY: 0.632 AC XY: 46916 AN XY: 74290

African (AFR) AF: 0.790 AC: 32790 AN: 41506

American (AMR) AF: 0.576 AC: 8793 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.659 AC: 2287 AN: 3472

East Asian (EAS) AF: 0.462 AC: 2380 AN: 5148

South Asian (SAS) AF: 0.513 AC: 2471 AN: 4816

European-Finnish (FIN) AF: 0.536 AC: 5654 AN: 10556

Middle Eastern (MID) AF: 0.612 AC: 180 AN: 294

European-Non Finnish (NFE) AF: 0.595 AC: 40439 AN: 67942

Other (OTH) AF: 0.635 AC: 1340 AN: 2110

Alfa AF: 0.607 Hom.: 106451

Bravo AF: 0.648

Asia WGS AF: 0.515 AC: 1791 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	4.1
DANN	Benign	0.69
PhyloP100		-0.33

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs6816070;

hg19: chr4-16480357;