rs16078

Variant names:

• chr7-24313836-G-A
• rs16078
• ENST00000718234.1:n.319+5521C>T

Your query was ambiguous. Multiple possible variants found:

• chr7-24313836-G-A
• chr7-24313836-G-C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The ENST00000718234.1(ENSG00000228944):​n.319+5521C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.03 in 152,244 control chromosomes in the GnomAD database, including 91 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 0.030 (91 hom., cov: 33)
• Consequence: ENSG00000228944 ENST00000718234.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00600
• Publications: 0 publications found

Genes affected

ENSG00000228944 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BS1: Variant frequency is greater than expected in population nfe. GnomAd4 allele frequency = 0.03 (4560/152244) while in subpopulation NFE AF = 0.0419 (2848/68004). AF 95% confidence interval is 0.0406. There are 91 homozygotes in GnomAd4. There are 2201 alleles in the male GnomAd4 subpopulation. Median coverage is 33. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 91 gene

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000718234.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000228944	ENST00000718234.1		n.319+5521C>T		intron	N/A
	ENSG00000228944	ENST00000745512.1		n.341+5521C>T		intron	N/A
	ENSG00000228944	ENST00000745513.1		n.309+5521C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0300 AC: 4562 AN: 152128 Hom.: 91 Cov.: 33

Gnomad AFR AF: 0.0159

Gnomad AMI AF: 0.00440

Gnomad AMR AF: 0.0224

Gnomad ASJ AF: 0.0156

Gnomad EAS AF: 0.000578

Gnomad SAS AF: 0.0286

Gnomad FIN AF: 0.0411

Gnomad MID AF: 0.0158

Gnomad NFE AF: 0.0419

Gnomad OTH AF: 0.0350

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

GnomAD4 genome AF: 0.0300 AC: 4560 AN: 152244 Hom.: 91 Cov.: 33 AF XY: 0.0296 AC XY: 2201 AN XY: 74450

African (AFR) AF: 0.0159 AC: 660 AN: 41554

American (AMR) AF: 0.0223 AC: 341 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.0156 AC: 54 AN: 3468

East Asian (EAS) AF: 0.000579 AC: 3 AN: 5182

South Asian (SAS) AF: 0.0286 AC: 138 AN: 4818

European-Finnish (FIN) AF: 0.0411 AC: 436 AN: 10606

Middle Eastern (MID) AF: 0.0102 AC: 3 AN: 294

European-Non Finnish (NFE) AF: 0.0419 AC: 2848 AN: 68004

Other (OTH) AF: 0.0346 AC: 73 AN: 2110

Alfa AF: 0.0406 Hom.: 17

Bravo AF: 0.0271

Asia WGS AF: 0.0110 AC: 38 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	1.0
DANN	Benign	0.68
PhyloP100		0.0060

Splicing

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

Other links and lift over

dbSNP: rs16078; hg19: chr7-24353455;