rs7194356

Variant names:

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

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

ENSG00000259929 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC107984893	XR_001752092.3	n.219-591G>A		intron_variant	Intron 2 of 2
LOC107984893	XR_001752093.2	n.219-591G>A		intron_variant	Intron 2 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000259929	ENST00000567304.1	n.252-591G>A		intron_variant	Intron 2 of 2	4
ENSG00000259929	ENST00000569048.5	n.260-591G>A		intron_variant	Intron 2 of 3	5

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

Gnomad4 AFR AF: 0.0209

Gnomad4 AMR AF: 0.0596

Gnomad4 ASJ AF: 0.0746

Gnomad4 EAS AF: 0.00154

Gnomad4 SAS AF: 0.0633

Gnomad4 FIN AF: 0.103

Gnomad4 NFE AF: 0.118

Gnomad4 OTH AF: 0.0616

Alfa AF: 0.106 Hom.: 548

Bravo AF: 0.0701

Asia WGS AF: 0.0280 AC: 97 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7194356; hg19: chr16-18062136;