7-16715823-C-T

Variant names:

• chr7-16715823-C-T
• rs818489
• ENST00000418907.1:n.72+4004G>A

Variant summary

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

The ENST00000418907.1(ENSG00000235837):​n.72+4004G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.588 in 152,108 control chromosomes in the GnomAD database, including 28,172 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 0.59 (28172 hom., cov: 33)
• Consequence: ENSG00000235837 ENST00000418907.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0160
• Publications: 1 publications found

Genes affected

ENSG00000235837 (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 = 0.818 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000418907.1. 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
	ENSG00000235837	ENST00000418907.1	TSL:3	n.72+4004G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.587 AC: 89259 AN: 151990 Hom.: 28126 Cov.: 33

Gnomad AFR AF: 0.825

Gnomad AMI AF: 0.534

Gnomad AMR AF: 0.524

Gnomad ASJ AF: 0.498

Gnomad EAS AF: 0.257

Gnomad SAS AF: 0.425

Gnomad FIN AF: 0.487

Gnomad MID AF: 0.506

Gnomad NFE AF: 0.516

Gnomad OTH AF: 0.544

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

GnomAD4 genome AF: 0.588 AC: 89364 AN: 152108 Hom.: 28172 Cov.: 33 AF XY: 0.582 AC XY: 43301 AN XY: 74364

African (AFR) AF: 0.825 AC: 34274 AN: 41532

American (AMR) AF: 0.523 AC: 7995 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.498 AC: 1729 AN: 3470

East Asian (EAS) AF: 0.257 AC: 1331 AN: 5174

South Asian (SAS) AF: 0.424 AC: 2046 AN: 4824

European-Finnish (FIN) AF: 0.487 AC: 5135 AN: 10542

Middle Eastern (MID) AF: 0.510 AC: 150 AN: 294

European-Non Finnish (NFE) AF: 0.516 AC: 35071 AN: 67972

Other (OTH) AF: 0.544 AC: 1147 AN: 2108

Alfa AF: 0.523 Hom.: 25227

Bravo AF: 0.596

Asia WGS AF: 0.403 AC: 1401 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	2.1
DANN	Benign	0.62
PhyloP100		0.016

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: rs818489;

hg19: chr7-16755448;