rs1362620

Variant names:

• chr16-55654462-T-C
• rs1362620
• XR_007065075.1:n.516-523A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XR_007065075.1(LOC124903693):​n.516-523A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.75 in 152,088 control chromosomes in the GnomAD database, including 42,999 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 0.75 (42999 hom., cov: 32)
• Consequence: LOC124903693 XR_007065075.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.823
• Publications: 5 publications found

Genes affected

LOC124903693 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.806 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.750 AC: 113956 AN: 151970 Hom.: 42958 Cov.: 32

Gnomad AFR AF: 0.814

Gnomad AMI AF: 0.651

Gnomad AMR AF: 0.783

Gnomad ASJ AF: 0.707

Gnomad EAS AF: 0.711

Gnomad SAS AF: 0.728

Gnomad FIN AF: 0.736

Gnomad MID AF: 0.630

Gnomad NFE AF: 0.715

Gnomad OTH AF: 0.731

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

GnomAD4 genome AF: 0.750 AC: 114061 AN: 152088 Hom.: 42999 Cov.: 32 AF XY: 0.753 AC XY: 55992 AN XY: 74310

African (AFR) AF: 0.814 AC: 33762 AN: 41494

American (AMR) AF: 0.783 AC: 11978 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.707 AC: 2455 AN: 3472

East Asian (EAS) AF: 0.710 AC: 3653 AN: 5148

South Asian (SAS) AF: 0.729 AC: 3510 AN: 4818

European-Finnish (FIN) AF: 0.736 AC: 7774 AN: 10556

Middle Eastern (MID) AF: 0.639 AC: 188 AN: 294

European-Non Finnish (NFE) AF: 0.715 AC: 48596 AN: 67990

Other (OTH) AF: 0.734 AC: 1551 AN: 2112

Alfa AF: 0.729 Hom.: 8222

Bravo AF: 0.757

Asia WGS AF: 0.716 AC: 2489 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.8
DANN	Benign	0.44
PhyloP100		-0.82

Splicing

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

Other links and lift over

dbSNP: rs1362620; hg19: chr16-55688374; COSMIC: COSV54915595;