chr2-43078788-G-A

Position:

• chr2-43078788-G-A

Variant summary

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

The XM_047446566.1(LOC107985876):​c.-3907-6228C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.374 in 152,098 control chromosomes in the GnomAD database, including 10,910 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 0.37 (10910 hom., cov: 33)
• Consequence: LOC107985876 XM_047446566.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.161

Genes affected

LOC107985876 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.436 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC107985876	XM_047446566.1	c.-3907-6228C>T		intron_variant
LOC124907756	XR_007086299.1	n.226-404G>A		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.374 AC: 56868 AN: 151980 Hom.: 10913 Cov.: 33

Gnomad AFR AF: 0.441

Gnomad AMI AF: 0.308

Gnomad AMR AF: 0.290

Gnomad ASJ AF: 0.341

Gnomad EAS AF: 0.106

Gnomad SAS AF: 0.277

Gnomad FIN AF: 0.336

Gnomad MID AF: 0.446

Gnomad NFE AF: 0.388

Gnomad OTH AF: 0.368

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

GnomAD4 genome AF: 0.374 AC: 56888 AN: 152098 Hom.: 10910 Cov.: 33 AF XY: 0.367 AC XY: 27257 AN XY: 74364

Gnomad4 AFR AF: 0.441

Gnomad4 AMR AF: 0.290

Gnomad4 ASJ AF: 0.341

Gnomad4 EAS AF: 0.105

Gnomad4 SAS AF: 0.275

Gnomad4 FIN AF: 0.336

Gnomad4 NFE AF: 0.388

Gnomad4 OTH AF: 0.367

Alfa AF: 0.377 Hom.: 22476

Bravo AF: 0.372

Asia WGS AF: 0.206 AC: 717 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.68
DANN	Benign	0.36

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2374482; hg19: chr2-43305926;