rs914833

chr1-56426388-C-T

Variant summary

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

The ENST00000641035.1(ENSG00000260971):n.555+50745G>A 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 0.215 in 152,078 control chromosomes in the GnomAD database, including 3,818 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 0.22 (3818 hom., cov: 32)
• Consequence: ENST00000641035.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.00

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 = 0.292 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC124904185	XR_007066106.1	n.5451-13861G>A		intron_variant, non_coding_transcript_variant
LOC124904185	XR_007066104.1	n.7272+1966G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000641035.1	n.555+50745G>A		intron_variant, non_coding_transcript_variant
	ENST00000641346.1	c.*96-26121G>A		intron_variant, NMD_transcript_variant				A2
	ENST00000641415.1	c.*95+56875G>A		intron_variant, NMD_transcript_variant				A2

Frequencies

GnomAD3 genomes AF: 0.215 AC: 32660 AN: 151958 Hom.: 3800 Cov.: 32

Gnomad AFR AF: 0.296

Gnomad AMI AF: 0.134

Gnomad AMR AF: 0.172

Gnomad ASJ AF: 0.116

Gnomad EAS AF: 0.257

Gnomad SAS AF: 0.279

Gnomad FIN AF: 0.119

Gnomad MID AF: 0.250

Gnomad NFE AF: 0.189

Gnomad OTH AF: 0.202

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

GnomAD4 genome AF: 0.215 AC: 32719 AN: 152078 Hom.: 3818 Cov.: 32 AF XY: 0.213 AC XY: 15865 AN XY: 74338

Gnomad4 AFR AF: 0.296

Gnomad4 AMR AF: 0.171

Gnomad4 ASJ AF: 0.116

Gnomad4 EAS AF: 0.257

Gnomad4 SAS AF: 0.278

Gnomad4 FIN AF: 0.119

Gnomad4 NFE AF: 0.189

Gnomad4 OTH AF: 0.204

Alfa AF: 0.207 Hom.: 469

Bravo AF: 0.221

Asia WGS AF: 0.284 AC: 988 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
Cadd	Benign	1.8
Dann	Benign	0.65

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs914833; hg19: chr1-56892060;