ENST00000650684.1:n.1074-23913A>G

Variant names:

• chr6-126843427-T-C
• rs17563605
• ENST00000650684.1:n.1074-23913A>G

Variant summary

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

The ENST00000650684.1(ENSG00000286215):​n.1074-23913A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.18 in 152,058 control chromosomes in the GnomAD database, including 3,072 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 0.18 (3072 hom., cov: 32)
• Consequence: ENSG00000286215 ENST00000650684.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0930

Genes affected

ENSG00000286215 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.253 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
ENSG00000286215	ENST00000650684.1	n.1074-23913A>G		intron_variant	Intron 8 of 8
ENSG00000286215	ENST00000650727.1	n.1044-23913A>G		intron_variant	Intron 8 of 14
ENSG00000286215	ENST00000650823.1	n.1129-23913A>G		intron_variant	Intron 9 of 11

Frequencies

GnomAD3 genomes AF: 0.180 AC: 27367 AN: 151940 Hom.: 3062 Cov.: 32

Gnomad AFR AF: 0.0712

Gnomad AMI AF: 0.270

Gnomad AMR AF: 0.182

Gnomad ASJ AF: 0.167

Gnomad EAS AF: 0.0216

Gnomad SAS AF: 0.204

Gnomad FIN AF: 0.181

Gnomad MID AF: 0.133

Gnomad NFE AF: 0.256

Gnomad OTH AF: 0.178

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

GnomAD4 genome AF: 0.180 AC: 27389 AN: 152058 Hom.: 3072 Cov.: 32 AF XY: 0.175 AC XY: 12978 AN XY: 74344

Gnomad4 AFR AF: 0.0711

Gnomad4 AMR AF: 0.182

Gnomad4 ASJ AF: 0.167

Gnomad4 EAS AF: 0.0215

Gnomad4 SAS AF: 0.204

Gnomad4 FIN AF: 0.181

Gnomad4 NFE AF: 0.256

Gnomad4 OTH AF: 0.185

Alfa AF: 0.238 Hom.: 4281

Bravo AF: 0.173

Asia WGS AF: 0.156 AC: 543 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	3.0
DANN	Benign	0.60

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17563605; hg19: chr6-127164572;