rs16218

Variant names:

• chr7-24218036-C-A
• rs16218
• ENST00000439839.1:n.160-21007G>T

Your query was ambiguous. Multiple possible variants found:

• chr7-24218036-C-A
• chr7-24218036-C-G
• chr7-24218036-C-T

Variant summary

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

The ENST00000718234.1(ENSG00000228944):​n.320-21007G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.388 in 151,752 control chromosomes in the GnomAD database, including 12,713 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 0.39 (12713 hom., cov: 31)
• Consequence: ENSG00000228944 ENST00000718234.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.11
• Publications: 2 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=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.569 is higher than 0.05.

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

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
	ENSG00000228944	ENST00000439839.1	TSL:5	n.160-21007G>T		intron	N/A
	ENSG00000228944	ENST00000718234.1		n.320-21007G>T		intron	N/A
	ENSG00000228944	ENST00000745512.1		n.342-21007G>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.388 AC: 58780 AN: 151634 Hom.: 12682 Cov.: 31

Gnomad AFR AF: 0.574

Gnomad AMI AF: 0.246

Gnomad AMR AF: 0.398

Gnomad ASJ AF: 0.261

Gnomad EAS AF: 0.568

Gnomad SAS AF: 0.434

Gnomad FIN AF: 0.340

Gnomad MID AF: 0.266

Gnomad NFE AF: 0.271

Gnomad OTH AF: 0.378

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

GnomAD4 genome AF: 0.388 AC: 58868 AN: 151752 Hom.: 12713 Cov.: 31 AF XY: 0.394 AC XY: 29184 AN XY: 74142

African (AFR) AF: 0.575 AC: 23768 AN: 41356

American (AMR) AF: 0.398 AC: 6071 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.261 AC: 903 AN: 3462

East Asian (EAS) AF: 0.568 AC: 2920 AN: 5138

South Asian (SAS) AF: 0.435 AC: 2087 AN: 4802

European-Finnish (FIN) AF: 0.340 AC: 3584 AN: 10530

Middle Eastern (MID) AF: 0.269 AC: 79 AN: 294

European-Non Finnish (NFE) AF: 0.271 AC: 18436 AN: 67914

Other (OTH) AF: 0.380 AC: 797 AN: 2100

Alfa AF: 0.353 Hom.: 1810

Bravo AF: 0.400

Asia WGS AF: 0.504 AC: 1751 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	8.4
DANN	Benign	0.67
PhyloP100		1.1

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: rs16218;

hg19: chr7-24257655;