rs949978

Variant names:

• chr2-21727485-A-G
• rs949978
• ENST00000435237.1:n.194-71872A>G

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000435237.1(ENSG00000231204):​n.194-71872A>G variant causes a intron 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: ENSG00000231204 ENST00000435237.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.59
• Publications: 0 publications found

Genes affected

ENSG00000231204 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000231204	ENST00000435237.1	n.194-71872A>G		intron_variant	Intron 3 of 5	3
ENSG00000231204	ENST00000717099.1	n.556-71872A>G		intron_variant	Intron 5 of 6
ENSG00000231204	ENST00000753412.1	n.162+3A>G		splice_region_variant, intron_variant	Intron 3 of 5

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

African (AFR) AF: 0.175 AC: 7238 AN: 41472

American (AMR) AF: 0.0971 AC: 1481 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.113 AC: 390 AN: 3466

East Asian (EAS) AF: 0.0341 AC: 175 AN: 5130

South Asian (SAS) AF: 0.0559 AC: 269 AN: 4814

European-Finnish (FIN) AF: 0.0568 AC: 603 AN: 10616

Middle Eastern (MID) AF: 0.0993 AC: 29 AN: 292

European-Non Finnish (NFE) AF: 0.0819 AC: 5568 AN: 67952

Other (OTH) AF: 0.114 AC: 240 AN: 2112

Alfa AF: 0.0871 Hom.: 344

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
PhyloP100		2.6

Splicing

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

Other links and lift over

dbSNP: rs949978; hg19: chr2-21950357;