2-200964879-C-G

Position:

• chr2-200964879-C-G

Variant summary

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

The ENST00000413848.1(ENSG00000183308):​n.368+1249C>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 0.228 in 152,074 control chromosomes in the GnomAD database, including 4,717 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 0.23 (4717 hom., cov: 32)
• Consequence: ENST00000413848.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.143

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.37 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105373835	XR_007088050.1	n.199+1249C>G		intron_variant, non_coding_transcript_variant
LOC105373835	XR_923783.3	n.199+1249C>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000413848.1	n.368+1249C>G		intron_variant, non_coding_transcript_variant		3
	ENST00000332935.6	n.332+1249C>G		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.228 AC: 34603 AN: 151956 Hom.: 4710 Cov.: 32

Gnomad AFR AF: 0.375

Gnomad AMI AF: 0.170

Gnomad AMR AF: 0.170

Gnomad ASJ AF: 0.237

Gnomad EAS AF: 0.00886

Gnomad SAS AF: 0.0831

Gnomad FIN AF: 0.181

Gnomad MID AF: 0.133

Gnomad NFE AF: 0.186

Gnomad OTH AF: 0.222

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

GnomAD4 genome AF: 0.228 AC: 34646 AN: 152074 Hom.: 4717 Cov.: 32 AF XY: 0.223 AC XY: 16597 AN XY: 74336

Gnomad4 AFR AF: 0.375

Gnomad4 AMR AF: 0.170

Gnomad4 ASJ AF: 0.237

Gnomad4 EAS AF: 0.00888

Gnomad4 SAS AF: 0.0831

Gnomad4 FIN AF: 0.181

Gnomad4 NFE AF: 0.186

Gnomad4 OTH AF: 0.220

Alfa AF: 0.218 Hom.: 525

Bravo AF: 0.236

Asia WGS AF: 0.0710 AC: 248 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	1.9
DANN	Benign	0.42

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs874358; hg19: chr2-201829602;