rs730402

Positions:

• chr2-59867571-G-A
• chr2-59867571-G-C

Variant summary

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

The ENST00000606382.1(ENSG00000271955):​n.111-40300C>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 0.514 in 152,096 control chromosomes in the GnomAD database, including 20,670 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 0.51 (20670 hom., cov: 33)
• Consequence: ENST00000606382.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.106

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 (AFR) allele frequency at 95% confidence interval = 0.622 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
	ENST00000606382.1	n.111-40300C>T		intron_variant, non_coding_transcript_variant		5
	ENST00000650011.1	n.274-9007C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.514 AC: 78133 AN: 151978 Hom.: 20637 Cov.: 33

Gnomad AFR AF: 0.629

Gnomad AMI AF: 0.434

Gnomad AMR AF: 0.506

Gnomad ASJ AF: 0.457

Gnomad EAS AF: 0.409

Gnomad SAS AF: 0.443

Gnomad FIN AF: 0.511

Gnomad MID AF: 0.437

Gnomad NFE AF: 0.465

Gnomad OTH AF: 0.491

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

GnomAD4 genome AF: 0.514 AC: 78209 AN: 152096 Hom.: 20670 Cov.: 33 AF XY: 0.515 AC XY: 38284 AN XY: 74338

Gnomad4 AFR AF: 0.629

Gnomad4 AMR AF: 0.507

Gnomad4 ASJ AF: 0.457

Gnomad4 EAS AF: 0.409

Gnomad4 SAS AF: 0.444

Gnomad4 FIN AF: 0.511

Gnomad4 NFE AF: 0.465

Gnomad4 OTH AF: 0.486

Alfa AF: 0.466 Hom.: 22343

Bravo AF: 0.519

Asia WGS AF: 0.423 AC: 1470 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	4.9
DANN	Benign	0.63

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs730402; hg19: chr2-60094706;