chr2-40823983-A-C

Position:

• chr2-40823983-A-C

Variant summary

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

The XR_001739421.3(LOC105374497):​n.216+13189T>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 0.517 in 151,870 control chromosomes in the GnomAD database, including 22,326 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 0.52 (22326 hom., cov: 31)
• Consequence: LOC105374497 XR_001739421.3 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -4.44

Genes affected

LOC105374497 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.696 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105374497	XR_001739421.3	n.216+13189T>G		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.518 AC: 78550 AN: 151752 Hom.: 22326 Cov.: 31

Gnomad AFR AF: 0.294

Gnomad AMI AF: 0.677

Gnomad AMR AF: 0.453

Gnomad ASJ AF: 0.635

Gnomad EAS AF: 0.356

Gnomad SAS AF: 0.715

Gnomad FIN AF: 0.645

Gnomad MID AF: 0.680

Gnomad NFE AF: 0.637

Gnomad OTH AF: 0.534

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

GnomAD4 genome AF: 0.517 AC: 78584 AN: 151870 Hom.: 22326 Cov.: 31 AF XY: 0.520 AC XY: 38607 AN XY: 74224

Gnomad4 AFR AF: 0.294

Gnomad4 AMR AF: 0.453

Gnomad4 ASJ AF: 0.635

Gnomad4 EAS AF: 0.356

Gnomad4 SAS AF: 0.716

Gnomad4 FIN AF: 0.645

Gnomad4 NFE AF: 0.637

Gnomad4 OTH AF: 0.530

Alfa AF: 0.613 Hom.: 49111

Bravo AF: 0.488

Asia WGS AF: 0.491 AC: 1708 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.0070
DANN	Benign	0.47

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs764464; hg19: chr2-41051123;