1-173052209-T-C

Position:

• chr1-173052209-T-C

Variant summary

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

The ENST00000432694.2(ENSG00000224228):​n.666-11664T>C variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0639 in 152,176 control chromosomes in the GnomAD database, including 387 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 0.064 (387 hom., cov: 32)
• Consequence: ENST00000432694.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.360

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.113 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000432694.2	n.666-11664T>C		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.0638 AC: 9698 AN: 152058 Hom.: 387 Cov.: 32

Gnomad AFR AF: 0.116

Gnomad AMI AF: 0.0549

Gnomad AMR AF: 0.0661

Gnomad ASJ AF: 0.0462

Gnomad EAS AF: 0.0315

Gnomad SAS AF: 0.0896

Gnomad FIN AF: 0.0185

Gnomad MID AF: 0.0728

Gnomad NFE AF: 0.0402

Gnomad OTH AF: 0.0623

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

GnomAD4 genome AF: 0.0639 AC: 9717 AN: 152176 Hom.: 387 Cov.: 32 AF XY: 0.0631 AC XY: 4698 AN XY: 74406

Gnomad4 AFR AF: 0.116

Gnomad4 AMR AF: 0.0660

Gnomad4 ASJ AF: 0.0462

Gnomad4 EAS AF: 0.0312

Gnomad4 SAS AF: 0.0886

Gnomad4 FIN AF: 0.0185

Gnomad4 NFE AF: 0.0402

Gnomad4 OTH AF: 0.0678

Alfa AF: 0.0386 Hom.: 126

Bravo AF: 0.0683

Asia WGS AF: 0.0750 AC: 259 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.91
DANN	Benign	0.51

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7537126; hg19: chr1-173021349;