chr16-7969609-T-G

Variant names:

• chr16-7969609-T-G
• rs1395593
• ENST00000567103.2:n.381+37536A>C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000567103.2(ENSG00000260289):​n.381+37536A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.196 in 152,170 control chromosomes in the GnomAD database, including 3,195 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 0.20 (3195 hom., cov: 32)
• Consequence: ENSG00000260289 ENST00000567103.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.833

Genes affected

ENSG00000260289 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.238 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000260289	ENST00000567103.2	n.381+37536A>C		intron_variant	Intron 2 of 3	5
ENSG00000260289	ENST00000654046.1	n.414+37536A>C		intron_variant	Intron 2 of 3
ENSG00000260289	ENST00000670665.1	n.484+8220A>C		intron_variant	Intron 3 of 4

Frequencies

GnomAD3 genomes AF: 0.196 AC: 29792 AN: 152050 Hom.: 3197 Cov.: 32

Gnomad AFR AF: 0.116

Gnomad AMI AF: 0.198

Gnomad AMR AF: 0.203

Gnomad ASJ AF: 0.301

Gnomad EAS AF: 0.230

Gnomad SAS AF: 0.153

Gnomad FIN AF: 0.173

Gnomad MID AF: 0.223

Gnomad NFE AF: 0.241

Gnomad OTH AF: 0.212

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

GnomAD4 genome AF: 0.196 AC: 29782 AN: 152170 Hom.: 3195 Cov.: 32 AF XY: 0.194 AC XY: 14446 AN XY: 74398

Gnomad4 AFR AF: 0.115

Gnomad4 AMR AF: 0.203

Gnomad4 ASJ AF: 0.301

Gnomad4 EAS AF: 0.229

Gnomad4 SAS AF: 0.152

Gnomad4 FIN AF: 0.173

Gnomad4 NFE AF: 0.241

Gnomad4 OTH AF: 0.211

Alfa AF: 0.213 Hom.: 2724

Bravo AF: 0.196

Asia WGS AF: 0.189 AC: 657 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.18
DANN	Benign	0.53

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1395593; hg19: chr16-8019611;