rs776488

Variant names:

• chr2-165034223-A-C
• rs776488
• ENST00000414885.2:n.1154-43397A>C

Your query was ambiguous. Multiple possible variants found:

• chr2-165034223-A-C
• chr2-165034223-A-G

Variant summary

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

The ENST00000414885.2(ENSG00000236283):​n.1154-43397A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.243 in 152,044 control chromosomes in the GnomAD database, including 5,804 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 0.24 (5804 hom., cov: 32)
• Consequence: ENSG00000236283 ENST00000414885.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.331
• Publications: 9 publications found

Genes affected

ENSG00000236283 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.35 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000414885.2. 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
	ENSG00000236283	ENST00000414885.2	TSL:5	n.1154-43397A>C		intron	N/A
	ENSG00000236283	ENST00000431341.1	TSL:3	n.299+40649A>C		intron	N/A
	ENSG00000236283	ENST00000628085.2	TSL:5	n.218+40583A>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.243 AC: 36981 AN: 151926 Hom.: 5798 Cov.: 32

Gnomad AFR AF: 0.0657

Gnomad AMI AF: 0.388

Gnomad AMR AF: 0.244

Gnomad ASJ AF: 0.265

Gnomad EAS AF: 0.0178

Gnomad SAS AF: 0.147

Gnomad FIN AF: 0.363

Gnomad MID AF: 0.196

Gnomad NFE AF: 0.354

Gnomad OTH AF: 0.250

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

GnomAD4 genome AF: 0.243 AC: 36985 AN: 152044 Hom.: 5804 Cov.: 32 AF XY: 0.240 AC XY: 17864 AN XY: 74336

African (AFR) AF: 0.0655 AC: 2719 AN: 41518

American (AMR) AF: 0.244 AC: 3728 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.265 AC: 920 AN: 3466

East Asian (EAS) AF: 0.0180 AC: 93 AN: 5162

South Asian (SAS) AF: 0.148 AC: 710 AN: 4812

European-Finnish (FIN) AF: 0.363 AC: 3835 AN: 10560

Middle Eastern (MID) AF: 0.190 AC: 56 AN: 294

European-Non Finnish (NFE) AF: 0.354 AC: 24048 AN: 67938

Other (OTH) AF: 0.247 AC: 522 AN: 2116

Alfa AF: 0.309 Hom.: 23558

Bravo AF: 0.226

Asia WGS AF: 0.0810 AC: 284 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	4.6
DANN	Benign	0.74
PhyloP100		0.33

Splicing

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

Other links and lift over

dbSNP: rs776488; hg19: chr2-165890733;