2-77715718-T-C

Position:

• chr2-77715718-T-C

Variant summary

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

The ENST00000667782.1(ENSG00000227088):​n.574+25803A>G 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 0.421 in 151,744 control chromosomes in the GnomAD database, including 14,761 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 0.42 (14761 hom., cov: 32)
• Consequence: ENST00000667782.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0390

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.554 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
	ENST00000667782.1	n.574+25803A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.421 AC: 63866 AN: 151626 Hom.: 14763 Cov.: 32

Gnomad AFR AF: 0.228

Gnomad AMI AF: 0.498

Gnomad AMR AF: 0.414

Gnomad ASJ AF: 0.586

Gnomad EAS AF: 0.473

Gnomad SAS AF: 0.572

Gnomad FIN AF: 0.454

Gnomad MID AF: 0.519

Gnomad NFE AF: 0.510

Gnomad OTH AF: 0.447

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

GnomAD4 genome AF: 0.421 AC: 63882 AN: 151744 Hom.: 14761 Cov.: 32 AF XY: 0.419 AC XY: 31027 AN XY: 74132

Gnomad4 AFR AF: 0.228

Gnomad4 AMR AF: 0.414

Gnomad4 ASJ AF: 0.586

Gnomad4 EAS AF: 0.473

Gnomad4 SAS AF: 0.571

Gnomad4 FIN AF: 0.454

Gnomad4 NFE AF: 0.510

Gnomad4 OTH AF: 0.445

Alfa AF: 0.353 Hom.: 1342

Bravo AF: 0.406

Asia WGS AF: 0.555 AC: 1902 AN: 3432

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	5.5
DANN	Benign	0.80

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11126630; hg19: chr2-77942844;