2-75232542-A-G

Position:

• chr2-75232542-A-G

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_Strong BS2

The XR_001739546.2(LOC107985900):​n.34885T>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00665 in 152,260 control chromosomes in the GnomAD database, including 7 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 0.0067 (7 hom., cov: 32)
• Consequence: LOC107985900 XR_001739546.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0370

Genes affected

LOC107985900 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -8 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BS2: High Homozygotes in GnomAd4 at 7 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC107985900	XR_001739546.2	n.34885T>C		non_coding_transcript_exon_variant	2/2
		n.75232542A>G		intergenic_region
LOC105374811	NR_168009.1	n.373-43968A>G		intron_variant
LOC105374811	NR_168010.1	n.367-43968A>G		intron_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.00665 AC: 1012 AN: 152142 Hom.: 7 Cov.: 32

Gnomad AFR AF: 0.00205

Gnomad AMI AF: 0.00110

Gnomad AMR AF: 0.00524

Gnomad ASJ AF: 0.00433

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.0110

Gnomad FIN AF: 0.00622

Gnomad MID AF: 0.0222

Gnomad NFE AF: 0.00998

Gnomad OTH AF: 0.0125

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

GnomAD4 genome AF: 0.00665 AC: 1013 AN: 152260 Hom.: 7 Cov.: 32 AF XY: 0.00647 AC XY: 482 AN XY: 74442

Gnomad4 AFR AF: 0.00205

Gnomad4 AMR AF: 0.00529

Gnomad4 ASJ AF: 0.00433

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.0112

Gnomad4 FIN AF: 0.00622

Gnomad4 NFE AF: 0.00998

Gnomad4 OTH AF: 0.0123

Alfa AF: 0.00155 Hom.: 0

Bravo AF: 0.00647

Asia WGS AF: 0.00549 AC: 19 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	3.8
DANN	Benign	0.49

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs765684; hg19: chr2-75459668;