chr1-230539080-T-C

Position:

• chr1-230539080-T-C

Variant summary

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

The ENST00000689608.1(ENSG00000282564):​n.329+40114T>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 0.503 in 151,874 control chromosomes in the GnomAD database, including 19,649 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 0.50 (19649 hom., cov: 31)
• Consequence: ENST00000689608.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.306

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.587 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
	ENST00000689608.1	n.329+40114T>C		intron_variant, non_coding_transcript_variant
	ENST00000685406.1	n.242-37414T>C		intron_variant, non_coding_transcript_variant
	ENST00000692577.2	n.318+40114T>C		intron_variant, non_coding_transcript_variant
	ENST00000702785.1	n.263+40114T>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.503 AC: 76347 AN: 151758 Hom.: 19614 Cov.: 31

Gnomad AFR AF: 0.593

Gnomad AMI AF: 0.558

Gnomad AMR AF: 0.535

Gnomad ASJ AF: 0.458

Gnomad EAS AF: 0.587

Gnomad SAS AF: 0.573

Gnomad FIN AF: 0.455

Gnomad MID AF: 0.462

Gnomad NFE AF: 0.440

Gnomad OTH AF: 0.482

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

GnomAD4 genome AF: 0.503 AC: 76436 AN: 151874 Hom.: 19649 Cov.: 31 AF XY: 0.507 AC XY: 37607 AN XY: 74204

Gnomad4 AFR AF: 0.593

Gnomad4 AMR AF: 0.536

Gnomad4 ASJ AF: 0.458

Gnomad4 EAS AF: 0.588

Gnomad4 SAS AF: 0.572

Gnomad4 FIN AF: 0.455

Gnomad4 NFE AF: 0.440

Gnomad4 OTH AF: 0.484

Alfa AF: 0.454 Hom.: 28162

Bravo AF: 0.519

Asia WGS AF: 0.623 AC: 2168 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	4.3
DANN	Benign	0.49

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs701157; hg19: chr1-230674826;