chr2-41571899-C-T

Position:

• chr2-41571899-C-T

Variant summary

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

The XR_939997.3(LOC105374506):​n.6106G>A 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 0.716 in 152,110 control chromosomes in the GnomAD database, including 40,053 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 0.72 (40053 hom., cov: 32)
• Consequence: LOC105374506 XR_939997.3 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.683

Genes affected

LOC105374506 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.932 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105374506	XR_939997.3	n.6106G>A		non_coding_transcript_exon_variant	1/4

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.716 AC: 108795 AN: 151992 Hom.: 39987 Cov.: 32

Gnomad AFR AF: 0.874

Gnomad AMI AF: 0.580

Gnomad AMR AF: 0.740

Gnomad ASJ AF: 0.608

Gnomad EAS AF: 0.954

Gnomad SAS AF: 0.744

Gnomad FIN AF: 0.626

Gnomad MID AF: 0.665

Gnomad NFE AF: 0.615

Gnomad OTH AF: 0.711

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

GnomAD4 genome AF: 0.716 AC: 108924 AN: 152110 Hom.: 40053 Cov.: 32 AF XY: 0.719 AC XY: 53437 AN XY: 74342

Gnomad4 AFR AF: 0.874

Gnomad4 AMR AF: 0.741

Gnomad4 ASJ AF: 0.608

Gnomad4 EAS AF: 0.954

Gnomad4 SAS AF: 0.744

Gnomad4 FIN AF: 0.626

Gnomad4 NFE AF: 0.615

Gnomad4 OTH AF: 0.715

Alfa AF: 0.653 Hom.: 14515

Bravo AF: 0.732

Asia WGS AF: 0.853 AC: 2965 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.71
DANN	Benign	0.27

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2217363; hg19: chr2-41799039;