rs3917386

Positions:

• chr2-112822289-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The ENST00000670671.1(ENSG00000287937):​n.197+1972A>G 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 0.0248 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: ENST00000670671.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0130

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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 male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd4 at 92 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC124907871	XR_007087195.1	n.219+1972A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000670671.1	n.197+1972A>G		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.00387

Gnomad4 AMR AF: 0.0305

Gnomad4 ASJ AF: 0.0550

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.0224

Gnomad4 FIN AF: 0.109

Gnomad4 NFE AF: 0.0243

Gnomad4 OTH AF: 0.0156

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3917386; hg19: chr2-113579866;