rs17164201

Variant names:

• chr7-11276563-A-G
• rs17164201
• ENST00000421121.5:n.113+23338A>G

Variant summary

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

The ENST00000421121.5(ENSG00000230333):​n.113+23338A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0817 in 152,060 control chromosomes in the GnomAD database, including 545 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 0.082 (545 hom., cov: 32)
• Consequence: ENSG00000230333 ENST00000421121.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.01
• Publications: 6 publications found

Genes affected

ENSG00000230333 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.1 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
ENSG00000230333	ENST00000421121.5	n.113+23338A>G		intron_variant	Intron 1 of 2	1
ENSG00000230333	ENST00000428533.5	n.138+79119A>G		intron_variant	Intron 1 of 2	5
ENSG00000230333	ENST00000428967.5	n.497+28188A>G		intron_variant	Intron 4 of 4	4

Frequencies

GnomAD3 genomes AF: 0.0817 AC: 12411 AN: 151942 Hom.: 546 Cov.: 32

Gnomad AFR AF: 0.0606

Gnomad AMI AF: 0.0526

Gnomad AMR AF: 0.0852

Gnomad ASJ AF: 0.100

Gnomad EAS AF: 0.0196

Gnomad SAS AF: 0.0581

Gnomad FIN AF: 0.0615

Gnomad MID AF: 0.0918

Gnomad NFE AF: 0.102

Gnomad OTH AF: 0.0982

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

GnomAD4 genome AF: 0.0817 AC: 12430 AN: 152060 Hom.: 545 Cov.: 32 AF XY: 0.0784 AC XY: 5826 AN XY: 74316

African (AFR) AF: 0.0609 AC: 2529 AN: 41526

American (AMR) AF: 0.0855 AC: 1304 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.100 AC: 348 AN: 3470

East Asian (EAS) AF: 0.0196 AC: 101 AN: 5144

South Asian (SAS) AF: 0.0575 AC: 277 AN: 4818

European-Finnish (FIN) AF: 0.0615 AC: 652 AN: 10610

Middle Eastern (MID) AF: 0.0918 AC: 27 AN: 294

European-Non Finnish (NFE) AF: 0.102 AC: 6938 AN: 67918

Other (OTH) AF: 0.0976 AC: 206 AN: 2110

Alfa AF: 0.0953 Hom.: 1043

Bravo AF: 0.0842

Asia WGS AF: 0.0440 AC: 155 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	5.4
DANN	Benign	0.63
PhyloP100		1.0

Splicing

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

Other links and lift over

dbSNP: rs17164201; hg19: chr7-11316190;