chr2-59827875-C-T

Position:

• chr2-59827875-C-T

Variant summary

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

The ENST00000606382.1(ENSG00000271955):​n.111-604G>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 0.581 in 151,804 control chromosomes in the GnomAD database, including 26,012 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 (26012 hom., cov: 32)
• Consequence: ENST00000606382.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.196

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.634 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
	ENST00000606382.1	n.111-604G>A		intron_variant, non_coding_transcript_variant		5
	ENST00000650011.1	n.388-604G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.581 AC: 88120 AN: 151686 Hom.: 25967 Cov.: 32

Gnomad AFR AF: 0.640

Gnomad AMI AF: 0.496

Gnomad AMR AF: 0.548

Gnomad ASJ AF: 0.528

Gnomad EAS AF: 0.393

Gnomad SAS AF: 0.471

Gnomad FIN AF: 0.614

Gnomad MID AF: 0.440

Gnomad NFE AF: 0.575

Gnomad OTH AF: 0.560

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

GnomAD4 genome AF: 0.581 AC: 88212 AN: 151804 Hom.: 26012 Cov.: 32 AF XY: 0.579 AC XY: 42963 AN XY: 74182

Gnomad4 AFR AF: 0.640

Gnomad4 AMR AF: 0.549

Gnomad4 ASJ AF: 0.528

Gnomad4 EAS AF: 0.393

Gnomad4 SAS AF: 0.472

Gnomad4 FIN AF: 0.614

Gnomad4 NFE AF: 0.575

Gnomad4 OTH AF: 0.552

Alfa AF: 0.566 Hom.: 24927

Bravo AF: 0.583

Asia WGS AF: 0.445 AC: 1549 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.31
DANN	Benign	0.46

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1013344; hg19: chr2-60055010;