chr2-87327903-A-G

Variant names:

• chr2-87327903-A-G
• rs994046
• ENST00000664547.2:n.71-4207T>C

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BP4_Strong BS2

The ENST00000664547.2(ENSG00000287763):​n.71-4207T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.492 in 142,840 control chromosomes in the GnomAD database, including 17,895 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 0.49 (17895 hom., cov: 23)
• Consequence: ENSG00000287763 ENST00000664547.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.798
• Publications: 1 publications found

Genes affected

ENSG00000287763 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -8 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BS2: High Homozygotes in GnomAd4 at 17895 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000287763	ENST00000664547.2	n.71-4207T>C		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.492 AC: 70269 AN: 142720 Hom.: 17878 Cov.: 23

Gnomad AFR AF: 0.465

Gnomad AMI AF: 0.531

Gnomad AMR AF: 0.530

Gnomad ASJ AF: 0.404

Gnomad EAS AF: 0.167

Gnomad SAS AF: 0.576

Gnomad FIN AF: 0.468

Gnomad MID AF: 0.480

Gnomad NFE AF: 0.528

Gnomad OTH AF: 0.489

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

GnomAD4 genome AF: 0.492 AC: 70335 AN: 142840 Hom.: 17895 Cov.: 23 AF XY: 0.489 AC XY: 33878 AN XY: 69334

⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5.

African (AFR) AF: 0.465 AC: 17836 AN: 38364

American (AMR) AF: 0.529 AC: 7508 AN: 14180

Ashkenazi Jewish (ASJ) AF: 0.404 AC: 1347 AN: 3334

East Asian (EAS) AF: 0.167 AC: 837 AN: 5022

South Asian (SAS) AF: 0.578 AC: 2457 AN: 4252

European-Finnish (FIN) AF: 0.468 AC: 4593 AN: 9820

Middle Eastern (MID) AF: 0.489 AC: 135 AN: 276

European-Non Finnish (NFE) AF: 0.528 AC: 34242 AN: 64822

Other (OTH) AF: 0.483 AC: 921 AN: 1906

⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5. (p-value = 0), which strongly suggests a high chance of mosaicism in these individuals.

Alfa AF: 0.509 Hom.: 2419

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.31
DANN	Benign	0.59
PhyloP100		-0.80

Splicing

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

Other links and lift over

dbSNP: rs994046; hg19: chr2-87555026;