rs7194356

Variant names:

• chr16-17968279-C-T
• rs7194356
• ENST00000567304.1:n.252-591G>A

Variant summary

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

The ENST00000567304.1(ENSG00000259929):​n.252-591G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0771 in 152,178 control chromosomes in the GnomAD database, including 563 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 0.077 (563 hom., cov: 32)
• Consequence: ENSG00000259929 ENST00000567304.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.143
• Publications: 2 publications found

Genes affected

ENSG00000259929 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.77).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.116 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000567304.1. 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
	ENSG00000259929	ENST00000567304.1	TSL:4	n.252-591G>A		intron	N/A
	ENSG00000259929	ENST00000569048.5	TSL:5	n.260-591G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0771 AC: 11731 AN: 152060 Hom.: 563 Cov.: 32

Gnomad AFR AF: 0.0210

Gnomad AMI AF: 0.112

Gnomad AMR AF: 0.0598

Gnomad ASJ AF: 0.0746

Gnomad EAS AF: 0.00154

Gnomad SAS AF: 0.0633

Gnomad FIN AF: 0.103

Gnomad MID AF: 0.0443

Gnomad NFE AF: 0.118

Gnomad OTH AF: 0.0622

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

GnomAD4 genome AF: 0.0771 AC: 11729 AN: 152178 Hom.: 563 Cov.: 32 AF XY: 0.0744 AC XY: 5533 AN XY: 74412

African (AFR) AF: 0.0209 AC: 868 AN: 41528

American (AMR) AF: 0.0596 AC: 912 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.0746 AC: 259 AN: 3470

East Asian (EAS) AF: 0.00154 AC: 8 AN: 5182

South Asian (SAS) AF: 0.0633 AC: 305 AN: 4816

European-Finnish (FIN) AF: 0.103 AC: 1090 AN: 10592

Middle Eastern (MID) AF: 0.0408 AC: 12 AN: 294

European-Non Finnish (NFE) AF: 0.118 AC: 8043 AN: 67980

Other (OTH) AF: 0.0616 AC: 130 AN: 2112

Alfa AF: 0.0968 Hom.: 724

Bravo AF: 0.0701

Asia WGS AF: 0.0280 AC: 97 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
CADD	Benign	2.9
DANN	Benign	0.83
PhyloP100		0.14

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: rs7194356;

hg19: chr16-18062136;