ENST00000548144.1:n.264+3597T>G

Variant names:

• chr16-68082115-T-G
• rs2107369
• ENST00000548144.1:n.264+3597T>G

Variant summary

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

The ENST00000548144.1(ENSG00000261864):​n.264+3597T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.178 in 152,072 control chromosomes in the GnomAD database, including 2,729 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 0.18 (2729 hom., cov: 32)
• Consequence: ENSG00000261864 ENST00000548144.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.757
• Publications: 15 publications found

Genes affected

ENSG00000261864 (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 (AFR) allele frequency at 95% confidence interval = 0.261 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000548144.1. 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
	ENSG00000261864	ENST00000548144.1	TSL:5	n.264+3597T>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.178 AC: 27007 AN: 151954 Hom.: 2716 Cov.: 32

Gnomad AFR AF: 0.265

Gnomad AMI AF: 0.218

Gnomad AMR AF: 0.163

Gnomad ASJ AF: 0.178

Gnomad EAS AF: 0.0804

Gnomad SAS AF: 0.195

Gnomad FIN AF: 0.177

Gnomad MID AF: 0.149

Gnomad NFE AF: 0.134

Gnomad OTH AF: 0.176

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

GnomAD4 genome AF: 0.178 AC: 27055 AN: 152072 Hom.: 2729 Cov.: 32 AF XY: 0.181 AC XY: 13438 AN XY: 74348

African (AFR) AF: 0.266 AC: 11003 AN: 41438

American (AMR) AF: 0.163 AC: 2496 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.178 AC: 616 AN: 3470

East Asian (EAS) AF: 0.0806 AC: 417 AN: 5174

South Asian (SAS) AF: 0.195 AC: 939 AN: 4824

European-Finnish (FIN) AF: 0.177 AC: 1871 AN: 10578

Middle Eastern (MID) AF: 0.143 AC: 42 AN: 294

European-Non Finnish (NFE) AF: 0.134 AC: 9093 AN: 67970

Other (OTH) AF: 0.179 AC: 379 AN: 2112

Alfa AF: 0.162 Hom.: 450

Bravo AF: 0.179

Asia WGS AF: 0.194 AC: 675 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	2.7
DANN	Benign	0.82
PhyloP100		-0.76

Splicing

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

Other links and lift over

dbSNP: rs2107369; hg19: chr16-68116018;