ENST00000670671.2:n.222+1972A>G

Variant names:

• chr2-112822289-T-C
• rs3917386
• ENST00000670671.2:n.222+1972A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The ENST00000670671.2(ENSG00000287937):​n.222+1972A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0248 in 152,272 control chromosomes in the GnomAD database, including 92 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 0.025 (92 hom., cov: 32)
• Consequence: ENSG00000287937 ENST00000670671.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0130
• Publications: 2 publications found

Genes affected

ENSG00000287937 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BS1: Variant frequency is greater than expected in population amr. GnomAd4 allele frequency = 0.0248 (3772/152272) while in subpopulation AMR AF = 0.0305 (467/15298). AF 95% confidence interval is 0.0282. There are 92 homozygotes in GnomAd4. There are 2109 alleles in the male GnomAd4 subpopulation. Median coverage is 32. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 92 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124907871	XR_007087195.1	n.219+1972A>G		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000287937	ENST00000670671.2	n.222+1972A>G		intron_variant	Intron 1 of 1
ENSG00000299339	ENST00000762706.1	n.404+51393T>C		intron_variant	Intron 2 of 3
ENSG00000299339	ENST00000762707.1	n.499+51393T>C		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.0248 AC: 3768 AN: 152154 Hom.: 92 Cov.: 32

Gnomad AFR AF: 0.00388

Gnomad AMI AF: 0.00768

Gnomad AMR AF: 0.0302

Gnomad ASJ AF: 0.0550

Gnomad EAS AF: 0.000192

Gnomad SAS AF: 0.0226

Gnomad FIN AF: 0.109

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0243

Gnomad OTH AF: 0.0158

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

GnomAD4 genome AF: 0.0248 AC: 3772 AN: 152272 Hom.: 92 Cov.: 32 AF XY: 0.0283 AC XY: 2109 AN XY: 74438

African (AFR) AF: 0.00387 AC: 161 AN: 41570

American (AMR) AF: 0.0305 AC: 467 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.0550 AC: 191 AN: 3470

East Asian (EAS) AF: 0.00 AC: 0 AN: 5188

South Asian (SAS) AF: 0.0224 AC: 108 AN: 4820

European-Finnish (FIN) AF: 0.109 AC: 1150 AN: 10586

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 294

European-Non Finnish (NFE) AF: 0.0243 AC: 1655 AN: 68024

Other (OTH) AF: 0.0156 AC: 33 AN: 2110

Alfa AF: 0.0264 Hom.: 19

Bravo AF: 0.0179

Asia WGS AF: 0.00722 AC: 25 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	2.0
DANN	Benign	0.66
PhyloP100		-0.013

Splicing

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

Other links and lift over

dbSNP: rs3917386; hg19: chr2-113579866;