2-188969185-T-C

Variant summary

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

The XR_007087614.1(LOC105373791):n.242+1162A>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 0.608 in 152,000 control chromosomes in the GnomAD database, including 28,664 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 0.61 (28664 hom., cov: 32)
• Consequence: LOC105373791 XR_007087614.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.08

Genes affected

LOC105373791 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.66 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105373791	XR_007087614.1	n.242+1162A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.609 AC: 92429 AN: 151880 Hom.: 28655 Cov.: 32

Gnomad AFR AF: 0.477

Gnomad AMI AF: 0.681

Gnomad AMR AF: 0.612

Gnomad ASJ AF: 0.553

Gnomad EAS AF: 0.661

Gnomad SAS AF: 0.657

Gnomad FIN AF: 0.724

Gnomad MID AF: 0.519

Gnomad NFE AF: 0.665

Gnomad OTH AF: 0.578

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

GnomAD4 genome AF: 0.608 AC: 92476 AN: 152000 Hom.: 28664 Cov.: 32 AF XY: 0.612 AC XY: 45459 AN XY: 74318

Gnomad4 AFR AF: 0.477

Gnomad4 AMR AF: 0.612

Gnomad4 ASJ AF: 0.553

Gnomad4 EAS AF: 0.661

Gnomad4 SAS AF: 0.657

Gnomad4 FIN AF: 0.724

Gnomad4 NFE AF: 0.665

Gnomad4 OTH AF: 0.581

Alfa AF: 0.648 Hom.: 64558

Bravo AF: 0.592

Asia WGS AF: 0.673 AC: 2341 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	3.0
Dann	Benign	0.44

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6434304; hg19: chr2-189833911;