rs776488

Positions:

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

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000638199.1(ENSG00000236283):​n.1144-56897A>C variant causes a intron, non coding transcript 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: ENST00000638199.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.331

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000638199.1	n.1144-56897A>C		intron_variant, non_coding_transcript_variant		5

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

Gnomad4 AFR AF: 0.0655

Gnomad4 AMR AF: 0.244

Gnomad4 ASJ AF: 0.265

Gnomad4 EAS AF: 0.0180

Gnomad4 SAS AF: 0.148

Gnomad4 FIN AF: 0.363

Gnomad4 NFE AF: 0.354

Gnomad4 OTH AF: 0.247

Alfa AF: 0.313 Hom.: 8918

Bravo AF: 0.226

Asia WGS AF: 0.0810 AC: 284 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs776488; hg19: chr2-165890733;