chr2-75200118-G-A

Position:

• chr2-75200118-G-A

Variant summary

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

The NR_168009.1(LOC105374811):​n.372+43803G>A 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 0.0626 in 152,322 control chromosomes in the GnomAD database, including 338 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 0.063 (338 hom., cov: 33)
• Consequence: LOC105374811 NR_168009.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.834

Genes affected

LOC105374811 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.079 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105374811	NR_168009.1	n.372+43803G>A		intron_variant, non_coding_transcript_variant
LOC105374811	NR_168010.1	n.366+43803G>A		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.0626 AC: 9528 AN: 152204 Hom.: 339 Cov.: 33

Gnomad AFR AF: 0.0568

Gnomad AMI AF: 0.0241

Gnomad AMR AF: 0.0399

Gnomad ASJ AF: 0.0351

Gnomad EAS AF: 0.00829

Gnomad SAS AF: 0.0319

Gnomad FIN AF: 0.0533

Gnomad MID AF: 0.0823

Gnomad NFE AF: 0.0808

Gnomad OTH AF: 0.0630

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

GnomAD4 genome AF: 0.0626 AC: 9531 AN: 152322 Hom.: 338 Cov.: 33 AF XY: 0.0602 AC XY: 4485 AN XY: 74480

Gnomad4 AFR AF: 0.0568

Gnomad4 AMR AF: 0.0398

Gnomad4 ASJ AF: 0.0351

Gnomad4 EAS AF: 0.00831

Gnomad4 SAS AF: 0.0323

Gnomad4 FIN AF: 0.0533

Gnomad4 NFE AF: 0.0808

Gnomad4 OTH AF: 0.0633

Alfa AF: 0.0524 Hom.: 64

Bravo AF: 0.0622

Asia WGS AF: 0.0230 AC: 80 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	9.7
DANN	Benign	0.58

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs13384011; hg19: chr2-75427244;