rs2039759

Positions:

• chr1-193634339-C-T

Variant summary

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

The ENST00000656143.1(ENSG00000227240):​n.154-38871C>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 0.467 in 151,644 control chromosomes in the GnomAD database, including 18,193 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 0.47 (18193 hom., cov: 32)
• Consequence: ENST00000656143.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.637

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.793 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC124904475	XR_007066777.1	n.5234+160963C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000656143.1	n.154-38871C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.467 AC: 70778 AN: 151526 Hom.: 18197 Cov.: 32

Gnomad AFR AF: 0.268

Gnomad AMI AF: 0.509

Gnomad AMR AF: 0.581

Gnomad ASJ AF: 0.631

Gnomad EAS AF: 0.814

Gnomad SAS AF: 0.604

Gnomad FIN AF: 0.408

Gnomad MID AF: 0.547

Gnomad NFE AF: 0.525

Gnomad OTH AF: 0.515

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

GnomAD4 genome AF: 0.467 AC: 70796 AN: 151644 Hom.: 18193 Cov.: 32 AF XY: 0.469 AC XY: 34773 AN XY: 74102

Gnomad4 AFR AF: 0.268

Gnomad4 AMR AF: 0.581

Gnomad4 ASJ AF: 0.631

Gnomad4 EAS AF: 0.813

Gnomad4 SAS AF: 0.603

Gnomad4 FIN AF: 0.408

Gnomad4 NFE AF: 0.525

Gnomad4 OTH AF: 0.515

Alfa AF: 0.513 Hom.: 9414

Bravo AF: 0.477

Asia WGS AF: 0.647 AC: 2251 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	3.5
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: rs2039759; hg19: chr1-193603469;