chr2-102296204-C-A

Variant names:

• chr2-102296204-C-A
• rs951774
• ENST00000804381.1:n.369-368C>A

Variant summary

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

The ENST00000804381.1(ENSG00000304533):​n.369-368C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.164 in 151,740 control chromosomes in the GnomAD database, including 2,729 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 0.16 (2729 hom., cov: 31)
• Consequence: ENSG00000304533 ENST00000804381.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.483
• Publications: 11 publications found

Genes affected

ENSG00000304533 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.335 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000804381.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000304533	ENST00000804381.1		n.369-368C>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.164 AC: 24861 AN: 151622 Hom.: 2717 Cov.: 31

Gnomad AFR AF: 0.0774

Gnomad AMI AF: 0.193

Gnomad AMR AF: 0.327

Gnomad ASJ AF: 0.120

Gnomad EAS AF: 0.244

Gnomad SAS AF: 0.349

Gnomad FIN AF: 0.207

Gnomad MID AF: 0.127

Gnomad NFE AF: 0.156

Gnomad OTH AF: 0.164

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

GnomAD4 genome AF: 0.164 AC: 24880 AN: 151740 Hom.: 2729 Cov.: 31 AF XY: 0.173 AC XY: 12792 AN XY: 74150

African (AFR) AF: 0.0772 AC: 3193 AN: 41340

American (AMR) AF: 0.328 AC: 4998 AN: 15242

Ashkenazi Jewish (ASJ) AF: 0.120 AC: 417 AN: 3466

East Asian (EAS) AF: 0.244 AC: 1253 AN: 5144

South Asian (SAS) AF: 0.349 AC: 1676 AN: 4798

European-Finnish (FIN) AF: 0.207 AC: 2171 AN: 10510

Middle Eastern (MID) AF: 0.122 AC: 36 AN: 294

European-Non Finnish (NFE) AF: 0.156 AC: 10619 AN: 67928

Other (OTH) AF: 0.162 AC: 341 AN: 2106

Alfa AF: 0.154 Hom.: 2377

Bravo AF: 0.169

Asia WGS AF: 0.298 AC: 1036 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.63
DANN	Benign	0.30
PhyloP100		-0.48

Splicing

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

Other links and lift over

dbSNP: rs951774; hg19: chr2-102912664;