chr1-234680808-G-C

Position:

• chr1-234680808-G-C

Variant summary

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

The ENST00000664534.1(ENSG00000228044):​n.183-3G>C variant causes a splice region, splice polypyrimidine tract, intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.58 in 151,762 control chromosomes in the GnomAD database, including 26,460 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 0.58 (26404 hom., cov: 28)
  • Exomes 𝑓: 0.61 (56 hom.)
• Consequence: ENST00000664534.1 splice_region, splice_polypyrimidine_tract, intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.590

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.666 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105373208	XR_949287.4	n.446-1459C>G		intron_variant, non_coding_transcript_variant
LOC105373209	XR_949289.3	n.76-3G>C		splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant, non_coding_transcript_variant
LOC105373208	XR_007066951.1	n.1736-1459C>G		intron_variant, non_coding_transcript_variant
LOC105373209	XR_949288.3	n.167-3G>C		splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000442382.1	n.97-7818C>G		intron_variant, non_coding_transcript_variant		2
	ENST00000664534.1	n.183-3G>C		splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant, non_coding_transcript_variant
	ENST00000449012.1	n.110-3G>C		splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant, non_coding_transcript_variant		3
	ENST00000453568.1	n.32-3G>C		splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.580 AC: 87806 AN: 151374 Hom.: 26374 Cov.: 28

Gnomad AFR AF: 0.672

Gnomad AMI AF: 0.471

Gnomad AMR AF: 0.464

Gnomad ASJ AF: 0.528

Gnomad EAS AF: 0.165

Gnomad SAS AF: 0.438

Gnomad FIN AF: 0.540

Gnomad MID AF: 0.564

Gnomad NFE AF: 0.602

Gnomad OTH AF: 0.571

GnomAD4 exome AF: 0.611 AC: 165 AN: 270 Hom.: 56 Cov.: 0 AF XY: 0.610 AC XY: 100 AN XY: 164

Gnomad4 AFR exome AF: 1.00

Gnomad4 AMR exome AF: 1.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.750

Gnomad4 FIN exome AF: 0.488

Gnomad4 NFE exome AF: 0.675

Gnomad4 OTH exome AF: 0.500

GnomAD4 genome AF: 0.580 AC: 87877 AN: 151492 Hom.: 26404 Cov.: 28 AF XY: 0.569 AC XY: 42104 AN XY: 73970

Gnomad4 AFR AF: 0.673

Gnomad4 AMR AF: 0.463

Gnomad4 ASJ AF: 0.528

Gnomad4 EAS AF: 0.165

Gnomad4 SAS AF: 0.439

Gnomad4 FIN AF: 0.540

Gnomad4 NFE AF: 0.602

Gnomad4 OTH AF: 0.565

Alfa AF: 0.575 Hom.: 14385

Bravo AF: 0.580

Asia WGS AF: 0.305 AC: 1065 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.85
DANN	Benign	0.64

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs482329; hg19: chr1-234816554;