16-54643380-A-G

Variant names:

• chr16-54643380-A-G
• rs7193843
• ENST00000637560.1:n.138-10016T>C

Variant summary

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

The ENST00000763453.1(ENSG00000299428):​n.791+6624A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.852 in 152,210 control chromosomes in the GnomAD database, including 55,527 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 0.85 (55527 hom., cov: 32)
• Consequence: ENSG00000299428 ENST00000763453.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.450
• Publications: 4 publications found

Genes affected

ENSG00000283258 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.934 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000763453.1. 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
	ENSG00000283258	ENST00000637560.1	TSL:5	n.138-10016T>C		intron	N/A
	ENSG00000299428	ENST00000763453.1		n.791+6624A>G		intron	N/A
	ENSG00000299428	ENST00000763454.1		n.173+6624A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.852 AC: 129591 AN: 152092 Hom.: 55475 Cov.: 32

Gnomad AFR AF: 0.942

Gnomad AMI AF: 0.918

Gnomad AMR AF: 0.886

Gnomad ASJ AF: 0.820

Gnomad EAS AF: 0.846

Gnomad SAS AF: 0.907

Gnomad FIN AF: 0.784

Gnomad MID AF: 0.864

Gnomad NFE AF: 0.798

Gnomad OTH AF: 0.844

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

GnomAD4 genome AF: 0.852 AC: 129698 AN: 152210 Hom.: 55527 Cov.: 32 AF XY: 0.853 AC XY: 63442 AN XY: 74392

African (AFR) AF: 0.942 AC: 39135 AN: 41552

American (AMR) AF: 0.886 AC: 13544 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.820 AC: 2846 AN: 3472

East Asian (EAS) AF: 0.846 AC: 4362 AN: 5156

South Asian (SAS) AF: 0.906 AC: 4376 AN: 4830

European-Finnish (FIN) AF: 0.784 AC: 8309 AN: 10592

Middle Eastern (MID) AF: 0.864 AC: 254 AN: 294

European-Non Finnish (NFE) AF: 0.798 AC: 54258 AN: 68000

Other (OTH) AF: 0.840 AC: 1777 AN: 2116

Alfa AF: 0.819 Hom.: 114329

Bravo AF: 0.862

Asia WGS AF: 0.889 AC: 3089 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	3.7
DANN	Benign	0.86
PhyloP100		0.45

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: rs7193843;

hg19: chr16-54677292;