1-102212289-T-C

Position:

• chr1-102212289-T-C

Variant summary

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

The ENST00000447916.1(ENSG00000233359):​n.399-12292A>G 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 0.336 in 151,898 control chromosomes in the GnomAD database, including 8,901 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 0.34 (8901 hom., cov: 32)
• Consequence: ENST00000447916.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.812

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.548 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
	ENST00000447916.1	n.399-12292A>G		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.336 AC: 51029 AN: 151778 Hom.: 8885 Cov.: 32

Gnomad AFR AF: 0.338

Gnomad AMI AF: 0.360

Gnomad AMR AF: 0.384

Gnomad ASJ AF: 0.383

Gnomad EAS AF: 0.567

Gnomad SAS AF: 0.338

Gnomad FIN AF: 0.244

Gnomad MID AF: 0.389

Gnomad NFE AF: 0.318

Gnomad OTH AF: 0.346

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

GnomAD4 genome AF: 0.336 AC: 51086 AN: 151898 Hom.: 8901 Cov.: 32 AF XY: 0.336 AC XY: 24963 AN XY: 74228

Gnomad4 AFR AF: 0.339

Gnomad4 AMR AF: 0.385

Gnomad4 ASJ AF: 0.383

Gnomad4 EAS AF: 0.565

Gnomad4 SAS AF: 0.338

Gnomad4 FIN AF: 0.244

Gnomad4 NFE AF: 0.318

Gnomad4 OTH AF: 0.349

Alfa AF: 0.336 Hom.: 1045

Bravo AF: 0.350

Asia WGS AF: 0.464 AC: 1612 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	5.9
DANN	Benign	0.78

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1938355; hg19: chr1-102677845;