1-233858125-G-A

Position:

• chr1-233858125-G-A

Variant summary

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

The ENST00000655369.1(ENSG00000286666):​n.222+7024C>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 0.176 in 152,102 control chromosomes in the GnomAD database, including 2,942 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 0.18 (2942 hom., cov: 32)
• Consequence: ENST00000655369.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.01

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.31 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000655369.1	n.222+7024C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.176 AC: 26705 AN: 151984 Hom.: 2925 Cov.: 32

Gnomad AFR AF: 0.314

Gnomad AMI AF: 0.132

Gnomad AMR AF: 0.112

Gnomad ASJ AF: 0.152

Gnomad EAS AF: 0.226

Gnomad SAS AF: 0.159

Gnomad FIN AF: 0.103

Gnomad MID AF: 0.209

Gnomad NFE AF: 0.116

Gnomad OTH AF: 0.161

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

GnomAD4 genome AF: 0.176 AC: 26763 AN: 152102 Hom.: 2942 Cov.: 32 AF XY: 0.174 AC XY: 12926 AN XY: 74354

Gnomad4 AFR AF: 0.315

Gnomad4 AMR AF: 0.112

Gnomad4 ASJ AF: 0.152

Gnomad4 EAS AF: 0.226

Gnomad4 SAS AF: 0.160

Gnomad4 FIN AF: 0.103

Gnomad4 NFE AF: 0.116

Gnomad4 OTH AF: 0.165

Alfa AF: 0.125 Hom.: 2191

Bravo AF: 0.184

Asia WGS AF: 0.223 AC: 773 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	1.1
DANN	Benign	0.73

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2088108; hg19: chr1-233993871;