rs12070116

Positions:

• chr1-238280529-C-T

Variant summary

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

The ENST00000665394.1(ENSG00000234464):​n.193+4370C>T 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 0.0552 in 151,946 control chromosomes in the GnomAD database, including 637 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 0.055 (637 hom., cov: 32)
• Consequence: ENST00000665394.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.790

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.169 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
	ENST00000665394.1	n.193+4370C>T		intron_variant, non_coding_transcript_variant
	ENST00000422844.1	n.123+4370C>T		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.0552 AC: 8380 AN: 151830 Hom.: 638 Cov.: 32

Gnomad AFR AF: 0.172

Gnomad AMI AF: 0.00110

Gnomad AMR AF: 0.0235

Gnomad ASJ AF: 0.00807

Gnomad EAS AF: 0.00289

Gnomad SAS AF: 0.0233

Gnomad FIN AF: 0.00142

Gnomad MID AF: 0.0223

Gnomad NFE AF: 0.00936

Gnomad OTH AF: 0.0436

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

GnomAD4 genome AF: 0.0552 AC: 8392 AN: 151946 Hom.: 637 Cov.: 32 AF XY: 0.0534 AC XY: 3962 AN XY: 74238

Gnomad4 AFR AF: 0.172

Gnomad4 AMR AF: 0.0234

Gnomad4 ASJ AF: 0.00807

Gnomad4 EAS AF: 0.00290

Gnomad4 SAS AF: 0.0238

Gnomad4 FIN AF: 0.00142

Gnomad4 NFE AF: 0.00934

Gnomad4 OTH AF: 0.0427

Alfa AF: 0.0356 Hom.: 58

Bravo AF: 0.0617

Asia WGS AF: 0.0310 AC: 108 AN: 3462

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.33
DANN	Benign	0.47

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12070116; hg19: chr1-238443829;