rs1372878

Positions:

• chr2-59677430-G-A

Variant summary

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

The ENST00000412409.3(ENSG00000233891):​n.261+42146C>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 0.0633 in 152,202 control chromosomes in the GnomAD database, including 606 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 0.063 (606 hom., cov: 32)
• Consequence: ENST00000412409.3 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0980

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.347 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
	ENST00000412409.3	n.261+42146C>T		intron_variant, non_coding_transcript_variant		3
	ENST00000606382.1	n.236+149716C>T		intron_variant, non_coding_transcript_variant		5
	ENST00000435557.1	n.224-7882C>T		intron_variant, non_coding_transcript_variant		4

Frequencies

GnomAD3 genomes AF: 0.0633 AC: 9621 AN: 152084 Hom.: 605 Cov.: 32

Gnomad AFR AF: 0.0872

Gnomad AMI AF: 0.0165

Gnomad AMR AF: 0.0620

Gnomad ASJ AF: 0.0156

Gnomad EAS AF: 0.361

Gnomad SAS AF: 0.0903

Gnomad FIN AF: 0.0263

Gnomad MID AF: 0.0253

Gnomad NFE AF: 0.0338

Gnomad OTH AF: 0.0498

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

GnomAD4 genome AF: 0.0633 AC: 9635 AN: 152202 Hom.: 606 Cov.: 32 AF XY: 0.0653 AC XY: 4860 AN XY: 74420

Gnomad4 AFR AF: 0.0873

Gnomad4 AMR AF: 0.0619

Gnomad4 ASJ AF: 0.0156

Gnomad4 EAS AF: 0.361

Gnomad4 SAS AF: 0.0899

Gnomad4 FIN AF: 0.0263

Gnomad4 NFE AF: 0.0338

Gnomad4 OTH AF: 0.0540

Alfa AF: 0.0429 Hom.: 146

Bravo AF: 0.0679

Asia WGS AF: 0.173 AC: 599 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	3.2
DANN	Benign	0.69

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1372878; hg19: chr2-59904565;