16-62764948-G-T

Variant names:

• chr16-62764948-G-T
• rs2962462
• XR_933661.3:n.94-4044G>T

Variant summary

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

The XR_933661.3(LOC102723560):​n.94-4044G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.772 in 152,078 control chromosomes in the GnomAD database, including 45,640 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 0.77 (45640 hom., cov: 32)
• Consequence: LOC102723560 XR_933661.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0430

Genes affected

LOC102723560 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.815 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC102723560	XR_933661.3	n.94-4044G>T		intron_variant	Intron 2 of 3
LOC102723560	XR_933663.3	n.221-4044G>T		intron_variant	Intron 2 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.772 AC: 117356 AN: 151960 Hom.: 45599 Cov.: 32

Gnomad AFR AF: 0.823

Gnomad AMI AF: 0.857

Gnomad AMR AF: 0.644

Gnomad ASJ AF: 0.639

Gnomad EAS AF: 0.656

Gnomad SAS AF: 0.764

Gnomad FIN AF: 0.844

Gnomad MID AF: 0.697

Gnomad NFE AF: 0.775

Gnomad OTH AF: 0.756

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

GnomAD4 genome AF: 0.772 AC: 117448 AN: 152078 Hom.: 45640 Cov.: 32 AF XY: 0.772 AC XY: 57425 AN XY: 74342

Gnomad4 AFR AF: 0.823

Gnomad4 AMR AF: 0.644

Gnomad4 ASJ AF: 0.639

Gnomad4 EAS AF: 0.655

Gnomad4 SAS AF: 0.764

Gnomad4 FIN AF: 0.844

Gnomad4 NFE AF: 0.775

Gnomad4 OTH AF: 0.755

Alfa AF: 0.773 Hom.: 19914

Bravo AF: 0.759

Asia WGS AF: 0.704 AC: 2443 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	3.0
DANN	Benign	0.48

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2962462; hg19: chr16-62798852;