rs2015252

chr1-55407107-C-T

Variant summary

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

The ENST00000643167.1(ENSG00000234810):n.138+77682C>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 0.414 in 152,146 control chromosomes in the GnomAD database, including 13,679 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 0.41 (13679 hom., cov: 33)
• Consequence: ENST00000643167.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.475

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.499 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000643167.1	n.138+77682C>T		intron_variant, non_coding_transcript_variant
	ENST00000646341.1	n.158+45542C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.414 AC: 62967 AN: 152028 Hom.: 13667 Cov.: 33

Gnomad AFR AF: 0.298

Gnomad AMI AF: 0.273

Gnomad AMR AF: 0.508

Gnomad ASJ AF: 0.525

Gnomad EAS AF: 0.431

Gnomad SAS AF: 0.325

Gnomad FIN AF: 0.426

Gnomad MID AF: 0.429

Gnomad NFE AF: 0.462

Gnomad OTH AF: 0.444

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

GnomAD4 genome AF: 0.414 AC: 62995 AN: 152146 Hom.: 13679 Cov.: 33 AF XY: 0.413 AC XY: 30738 AN XY: 74384

Gnomad4 AFR AF: 0.298

Gnomad4 AMR AF: 0.508

Gnomad4 ASJ AF: 0.525

Gnomad4 EAS AF: 0.430

Gnomad4 SAS AF: 0.325

Gnomad4 FIN AF: 0.426

Gnomad4 NFE AF: 0.462

Gnomad4 OTH AF: 0.440

Alfa AF: 0.456 Hom.: 27052

Bravo AF: 0.414

Asia WGS AF: 0.363 AC: 1264 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
Cadd	Benign	0.39
Dann	Benign	0.24

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2015252; hg19: chr1-55872780;