2-219918601-C-T

Variant names:

• chr2-219918601-C-T
• rs4672960
• ENST00000803405.1:n.622C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000803405.1(ENSG00000304439):​n.622C>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.269 in 152,092 control chromosomes in the GnomAD database, including 5,861 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 0.27 (5861 hom., cov: 33)
• Consequence: ENSG00000304439 ENST00000803405.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.367
• Publications: 1 publications found

Genes affected

ENSG00000304439 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.305 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000803405.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000304439	ENST00000803405.1		n.622C>T		non_coding_transcript_exon	Exon 3 of 3
	ENSG00000304439	ENST00000803406.1		n.396C>T		non_coding_transcript_exon	Exon 3 of 3

Frequencies

GnomAD3 genomes AF: 0.269 AC: 40939 AN: 151972 Hom.: 5865 Cov.: 33

Gnomad AFR AF: 0.210

Gnomad AMI AF: 0.328

Gnomad AMR AF: 0.264

Gnomad ASJ AF: 0.295

Gnomad EAS AF: 0.0937

Gnomad SAS AF: 0.197

Gnomad FIN AF: 0.361

Gnomad MID AF: 0.326

Gnomad NFE AF: 0.308

Gnomad OTH AF: 0.282

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

GnomAD4 genome AF: 0.269 AC: 40937 AN: 152092 Hom.: 5861 Cov.: 33 AF XY: 0.267 AC XY: 19857 AN XY: 74328

African (AFR) AF: 0.210 AC: 8700 AN: 41472

American (AMR) AF: 0.264 AC: 4036 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.295 AC: 1024 AN: 3468

East Asian (EAS) AF: 0.0937 AC: 484 AN: 5164

South Asian (SAS) AF: 0.197 AC: 947 AN: 4812

European-Finnish (FIN) AF: 0.361 AC: 3817 AN: 10570

Middle Eastern (MID) AF: 0.310 AC: 91 AN: 294

European-Non Finnish (NFE) AF: 0.308 AC: 20946 AN: 67998

Other (OTH) AF: 0.281 AC: 593 AN: 2110

Alfa AF: 0.291 Hom.: 20637

Bravo AF: 0.258

Asia WGS AF: 0.152 AC: 530 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.17
DANN	Benign	0.41
PhyloP100		-0.37

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs4672960;

hg19: chr2-220783322;