chr2-81824988-T-C

Position:

• chr2-81824988-T-C

Variant summary

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

The XR_007088668.1(LOC102724542):​n.668-23765T>C 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 0.758 in 151,946 control chromosomes in the GnomAD database, including 43,871 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 0.76 (43871 hom., cov: 31)
• Consequence: LOC102724542 XR_007088668.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00

Genes affected

LOC102724542 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.784 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC102724542	XR_007088668.1	n.668-23765T>C		intron_variant, non_coding_transcript_variant
LOC102724542	XR_940294.2	n.576-23765T>C		intron_variant, non_coding_transcript_variant
LOC102724542	XR_940295.2	n.498-23765T>C		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.758 AC: 115142 AN: 151828 Hom.: 43827 Cov.: 31

Gnomad AFR AF: 0.729

Gnomad AMI AF: 0.887

Gnomad AMR AF: 0.755

Gnomad ASJ AF: 0.869

Gnomad EAS AF: 0.625

Gnomad SAS AF: 0.693

Gnomad FIN AF: 0.723

Gnomad MID AF: 0.811

Gnomad NFE AF: 0.790

Gnomad OTH AF: 0.756

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

GnomAD4 genome AF: 0.758 AC: 115241 AN: 151946 Hom.: 43871 Cov.: 31 AF XY: 0.751 AC XY: 55766 AN XY: 74258

Gnomad4 AFR AF: 0.729

Gnomad4 AMR AF: 0.754

Gnomad4 ASJ AF: 0.869

Gnomad4 EAS AF: 0.625

Gnomad4 SAS AF: 0.694

Gnomad4 FIN AF: 0.723

Gnomad4 NFE AF: 0.790

Gnomad4 OTH AF: 0.757

Alfa AF: 0.788 Hom.: 89527

Bravo AF: 0.759

Asia WGS AF: 0.685 AC: 2382 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	4.8
DANN	Benign	0.39

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1432170; hg19: chr2-82052112;