16-71244565-A-G

Variant names:

• chr16-71244565-A-G
• rs1018910
• ENST00000751566.1:n.90-2965A>G

Variant summary

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

The ENST00000751566.1(ENSG00000297892):​n.90-2965A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.326 in 152,086 control chromosomes in the GnomAD database, including 8,877 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 0.33 (8877 hom., cov: 32)
• Consequence: ENSG00000297892 ENST00000751566.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.215
• Publications: 4 publications found

Genes affected

ENSG00000297892 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.447 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000751566.1. 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
	ENSG00000297892	ENST00000751566.1		n.90-2965A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.326 AC: 49560 AN: 151968 Hom.: 8840 Cov.: 32

Gnomad AFR AF: 0.447

Gnomad AMI AF: 0.224

Gnomad AMR AF: 0.455

Gnomad ASJ AF: 0.298

Gnomad EAS AF: 0.238

Gnomad SAS AF: 0.214

Gnomad FIN AF: 0.226

Gnomad MID AF: 0.342

Gnomad NFE AF: 0.257

Gnomad OTH AF: 0.311

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

GnomAD4 genome AF: 0.326 AC: 49652 AN: 152086 Hom.: 8877 Cov.: 32 AF XY: 0.325 AC XY: 24135 AN XY: 74346

African (AFR) AF: 0.448 AC: 18559 AN: 41462

American (AMR) AF: 0.456 AC: 6970 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.298 AC: 1036 AN: 3472

East Asian (EAS) AF: 0.237 AC: 1225 AN: 5164

South Asian (SAS) AF: 0.213 AC: 1028 AN: 4832

European-Finnish (FIN) AF: 0.226 AC: 2395 AN: 10584

Middle Eastern (MID) AF: 0.333 AC: 98 AN: 294

European-Non Finnish (NFE) AF: 0.257 AC: 17469 AN: 67972

Other (OTH) AF: 0.316 AC: 668 AN: 2112

Alfa AF: 0.313 Hom.: 1485

Bravo AF: 0.353

Asia WGS AF: 0.289 AC: 1005 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	9.8
DANN	Benign	0.72
PhyloP100		0.21

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: rs1018910;

hg19: chr16-71278468;