rs2962457

Positions:

• chr16-62815673-C-G

Variant summary

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

The XR_933663.3(LOC102723560):​n.314-19887C>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 0.777 in 152,088 control chromosomes in the GnomAD database, including 46,252 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 0.78 (46252 hom., cov: 31)
• Consequence: LOC102723560 XR_933663.3 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.11

Genes affected

LOC102723560 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.821 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC102723560	XR_933663.3	n.314-19887C>G		intron_variant, non_coding_transcript_variant
LOC102723560	XR_933661.3	n.187-19887C>G		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.777 AC: 118127 AN: 151970 Hom.: 46200 Cov.: 31

Gnomad AFR AF: 0.828

Gnomad AMI AF: 0.858

Gnomad AMR AF: 0.653

Gnomad ASJ AF: 0.681

Gnomad EAS AF: 0.637

Gnomad SAS AF: 0.759

Gnomad FIN AF: 0.827

Gnomad MID AF: 0.718

Gnomad NFE AF: 0.783

Gnomad OTH AF: 0.759

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

GnomAD4 genome AF: 0.777 AC: 118232 AN: 152088 Hom.: 46252 Cov.: 31 AF XY: 0.777 AC XY: 57770 AN XY: 74346

Gnomad4 AFR AF: 0.828

Gnomad4 AMR AF: 0.653

Gnomad4 ASJ AF: 0.681

Gnomad4 EAS AF: 0.636

Gnomad4 SAS AF: 0.759

Gnomad4 FIN AF: 0.827

Gnomad4 NFE AF: 0.783

Gnomad4 OTH AF: 0.759

Alfa AF: 0.776 Hom.: 5698

Bravo AF: 0.766

Asia WGS AF: 0.688 AC: 2393 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.19
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: rs2962457; hg19: chr16-62849577;