rs17563605

Variant names:

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

Variant summary

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

The ENST00000650684.1(ENSG00000293110):​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: ENSG00000293110 ENST00000650684.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0930
• Publications: 10 publications found

Genes affected

ENSG00000293110 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000650684.1. 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
	ENSG00000293110	ENST00000650684.1		n.1074-23913A>G		intron	N/A
	ENSG00000293110	ENST00000650727.1		n.1044-23913A>G		intron	N/A
	ENSG00000293110	ENST00000650823.1		n.1129-23913A>G		intron	N/A

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

African (AFR) AF: 0.0711 AC: 2952 AN: 41536

American (AMR) AF: 0.182 AC: 2778 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.167 AC: 579 AN: 3464

East Asian (EAS) AF: 0.0215 AC: 111 AN: 5172

South Asian (SAS) AF: 0.204 AC: 983 AN: 4826

European-Finnish (FIN) AF: 0.181 AC: 1915 AN: 10598

Middle Eastern (MID) AF: 0.126 AC: 37 AN: 294

European-Non Finnish (NFE) AF: 0.256 AC: 17398 AN: 67886

Other (OTH) AF: 0.185 AC: 390 AN: 2104

Alfa AF: 0.236 Hom.: 4813

Bravo AF: 0.173

Asia WGS AF: 0.156 AC: 543 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	3.0
DANN	Benign	0.60
PhyloP100		0.093

Splicing

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

Other links and lift over

dbSNP: rs17563605; hg19: chr6-127164572;