2-54432570-C-G

Variant names:

• chr2-54432570-C-G
• rs4233949
• XR_001739475.2:n.207C>G

Variant summary

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

The XR_001739475.2(LOC102724072):​n.207C>G 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 0.666 in 152,102 control chromosomes in the GnomAD database, including 34,137 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 0.67 (34137 hom., cov: 32)
• Consequence: LOC102724072 XR_001739475.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.379
• Publications: 37 publications found

Genes affected

LOC102724072 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.943 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC102724072	XR_001739475.2	n.207C>G		non_coding_transcript_exon_variant	Exon 1 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000304706	ENST00000805723.1	n.45-10209G>C		intron_variant	Intron 1 of 1
ENSG00000304731	ENST00000805831.1	n.262-292C>G		intron_variant	Intron 2 of 7
ENSG00000304731	ENST00000805832.1	n.284-292C>G		intron_variant	Intron 2 of 7

Frequencies

GnomAD3 genomes AF: 0.666 AC: 101184 AN: 151984 Hom.: 34109 Cov.: 32

Gnomad AFR AF: 0.685

Gnomad AMI AF: 0.691

Gnomad AMR AF: 0.725

Gnomad ASJ AF: 0.573

Gnomad EAS AF: 0.965

Gnomad SAS AF: 0.705

Gnomad FIN AF: 0.724

Gnomad MID AF: 0.630

Gnomad NFE AF: 0.611

Gnomad OTH AF: 0.637

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

GnomAD4 genome AF: 0.666 AC: 101259 AN: 152102 Hom.: 34137 Cov.: 32 AF XY: 0.675 AC XY: 50180 AN XY: 74338

African (AFR) AF: 0.685 AC: 28428 AN: 41476

American (AMR) AF: 0.726 AC: 11093 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.573 AC: 1987 AN: 3468

East Asian (EAS) AF: 0.965 AC: 4998 AN: 5180

South Asian (SAS) AF: 0.706 AC: 3405 AN: 4826

European-Finnish (FIN) AF: 0.724 AC: 7658 AN: 10572

Middle Eastern (MID) AF: 0.609 AC: 179 AN: 294

European-Non Finnish (NFE) AF: 0.611 AC: 41551 AN: 67980

Other (OTH) AF: 0.632 AC: 1330 AN: 2104

Alfa AF: 0.609 Hom.: 14161

Bravo AF: 0.667

Asia WGS AF: 0.812 AC: 2818 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	7.4
DANN	Benign	0.67
PhyloP100		0.38

Splicing

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

Other links and lift over

dbSNP: rs4233949; hg19: chr2-54659707;