chr2-21617221-C-T

Position:

• chr2-21617221-C-T

Variant summary

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

The ENST00000435237.1(ENSG00000233005):​n.193+87978C>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 0.849 in 152,064 control chromosomes in the GnomAD database, including 57,006 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 0.85 (57006 hom., cov: 31)
• Consequence: ENST00000435237.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.719

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.961 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC101929230	XR_001739327.2	n.2803-9311G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000435237.1	n.193+87978C>T		intron_variant, non_coding_transcript_variant		3
	ENST00000648747.1	n.1032-9311G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.849 AC: 129032 AN: 151946 Hom.: 56991 Cov.: 31

Gnomad AFR AF: 0.582

Gnomad AMI AF: 0.993

Gnomad AMR AF: 0.887

Gnomad ASJ AF: 0.962

Gnomad EAS AF: 0.858

Gnomad SAS AF: 0.944

Gnomad FIN AF: 0.977

Gnomad MID AF: 0.930

Gnomad NFE AF: 0.967

Gnomad OTH AF: 0.865

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

GnomAD4 genome AF: 0.849 AC: 129076 AN: 152064 Hom.: 57006 Cov.: 31 AF XY: 0.851 AC XY: 63268 AN XY: 74336

Gnomad4 AFR AF: 0.581

Gnomad4 AMR AF: 0.887

Gnomad4 ASJ AF: 0.962

Gnomad4 EAS AF: 0.858

Gnomad4 SAS AF: 0.945

Gnomad4 FIN AF: 0.977

Gnomad4 NFE AF: 0.967

Gnomad4 OTH AF: 0.866

Alfa AF: 0.944 Hom.: 82911

Bravo AF: 0.829

Asia WGS AF: 0.868 AC: 3019 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.57
DANN	Benign	0.76

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1117324; hg19: chr2-21840093;