2-199889178-T-C

Position:

• chr2-199889178-T-C

Variant summary

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

The ENST00000457577.7(ENSG00000232732):​n.351+19925A>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 0.83 in 152,000 control chromosomes in the GnomAD database, including 52,383 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 0.83 (52383 hom., cov: 30)
• Consequence: ENST00000457577.7 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.41

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 (SAS) allele frequency at 95% confidence interval = 0.885 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC101927687	XR_923766.4	n.193-9568A>G		intron_variant, non_coding_transcript_variant
LOC101927687	XR_923769.4	n.193-6582A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000457577.7	n.351+19925A>G		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.830 AC: 125990 AN: 151882 Hom.: 52327 Cov.: 30

Gnomad AFR AF: 0.846

Gnomad AMI AF: 0.868

Gnomad AMR AF: 0.897

Gnomad ASJ AF: 0.868

Gnomad EAS AF: 0.795

Gnomad SAS AF: 0.907

Gnomad FIN AF: 0.744

Gnomad MID AF: 0.886

Gnomad NFE AF: 0.811

Gnomad OTH AF: 0.843

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

GnomAD4 genome AF: 0.830 AC: 126104 AN: 152000 Hom.: 52383 Cov.: 30 AF XY: 0.830 AC XY: 61638 AN XY: 74268

Gnomad4 AFR AF: 0.847

Gnomad4 AMR AF: 0.897

Gnomad4 ASJ AF: 0.868

Gnomad4 EAS AF: 0.795

Gnomad4 SAS AF: 0.908

Gnomad4 FIN AF: 0.744

Gnomad4 NFE AF: 0.811

Gnomad4 OTH AF: 0.843

Alfa AF: 0.810 Hom.: 6194

Bravo AF: 0.840

Asia WGS AF: 0.855 AC: 2975 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	0.20
DANN	Benign	0.39

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs166848; hg19: chr2-200753901;