rs175969

Variant names:

• chr1-28872046-T-C
• rs175969
• ENST00000418471.1:n.565+194A>G

Variant summary

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

The ENST00000418471.1(ENSG00000233427):​n.565+194A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.107 in 152,076 control chromosomes in the GnomAD database, including 1,016 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 0.11 (1016 hom., cov: 30)
• Consequence: ENSG00000233427 ENST00000418471.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.474

Genes affected

ENSG00000233427 (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 (AFR) allele frequency at 95% confidence interval = 0.156 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
ENSG00000233427	ENST00000418471.1	n.565+194A>G		intron_variant	Intron 2 of 2	5

Frequencies

GnomAD3 genomes AF: 0.107 AC: 16200 AN: 151958 Hom.: 1013 Cov.: 30

Gnomad AFR AF: 0.160

Gnomad AMI AF: 0.0581

Gnomad AMR AF: 0.101

Gnomad ASJ AF: 0.117

Gnomad EAS AF: 0.125

Gnomad SAS AF: 0.153

Gnomad FIN AF: 0.0816

Gnomad MID AF: 0.136

Gnomad NFE AF: 0.0743

Gnomad OTH AF: 0.122

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

GnomAD4 genome AF: 0.107 AC: 16210 AN: 152076 Hom.: 1016 Cov.: 30 AF XY: 0.109 AC XY: 8070 AN XY: 74342

Gnomad4 AFR AF: 0.160

Gnomad4 AMR AF: 0.101

Gnomad4 ASJ AF: 0.117

Gnomad4 EAS AF: 0.126

Gnomad4 SAS AF: 0.153

Gnomad4 FIN AF: 0.0816

Gnomad4 NFE AF: 0.0742

Gnomad4 OTH AF: 0.121

Alfa AF: 0.0974 Hom.: 93

Bravo AF: 0.109

Asia WGS AF: 0.158 AC: 549 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	4.7
DANN	Benign	0.45

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs175969; hg19: chr1-29198558;