rs949978

chr2-21727485-A-G

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000435237.1(ENSG00000233005):n.194-71872A>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 0.105 in 152,010 control chromosomes in the GnomAD database, including 1,015 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 0.11 (1015 hom., cov: 32)
• Consequence: ENST00000435237.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.59

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.42).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.171 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000435237.1	n.194-71872A>G		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.105 AC: 15995 AN: 151890 Hom.: 1006 Cov.: 32

Gnomad AFR AF: 0.174

Gnomad AMI AF: 0.0407

Gnomad AMR AF: 0.0974

Gnomad ASJ AF: 0.113

Gnomad EAS AF: 0.0340

Gnomad SAS AF: 0.0560

Gnomad FIN AF: 0.0568

Gnomad MID AF: 0.105

Gnomad NFE AF: 0.0820

Gnomad OTH AF: 0.115

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

GnomAD4 genome AF: 0.105 AC: 16030 AN: 152010 Hom.: 1015 Cov.: 32 AF XY: 0.103 AC XY: 7679 AN XY: 74298

Gnomad4 AFR AF: 0.175

Gnomad4 AMR AF: 0.0971

Gnomad4 ASJ AF: 0.113

Gnomad4 EAS AF: 0.0341

Gnomad4 SAS AF: 0.0559

Gnomad4 FIN AF: 0.0568

Gnomad4 NFE AF: 0.0819

Gnomad4 OTH AF: 0.114

Alfa AF: 0.0865 Hom.: 309

Bravo AF: 0.112

Asia WGS AF: 0.0700 AC: 245 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.42
Cadd	Benign	19
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: rs949978; hg19: chr2-21950357;