rs16212

chr7-24225042-C-G

Variant summary

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

The ENST00000439839.1(ENSG00000228944):n.160-28013G>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 0.0564 in 152,238 control chromosomes in the GnomAD database, including 295 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 0.056 (295 hom., cov: 32)
• Consequence: ENST00000439839.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.135

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.51).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.132 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC107986777	XR_001745132.2	n.210-28013G>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000439839.1	n.160-28013G>C		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.0564 AC: 8572 AN: 152120 Hom.: 293 Cov.: 32

Gnomad AFR AF: 0.0893

Gnomad AMI AF: 0.0197

Gnomad AMR AF: 0.0569

Gnomad ASJ AF: 0.0262

Gnomad EAS AF: 0.141

Gnomad SAS AF: 0.0487

Gnomad FIN AF: 0.0268

Gnomad MID AF: 0.0158

Gnomad NFE AF: 0.0372

Gnomad OTH AF: 0.0517

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

GnomAD4 genome AF: 0.0564 AC: 8586 AN: 152238 Hom.: 295 Cov.: 32 AF XY: 0.0561 AC XY: 4176 AN XY: 74442

Gnomad4 AFR AF: 0.0893

Gnomad4 AMR AF: 0.0572

Gnomad4 ASJ AF: 0.0262

Gnomad4 EAS AF: 0.141

Gnomad4 SAS AF: 0.0485

Gnomad4 FIN AF: 0.0268

Gnomad4 NFE AF: 0.0372

Gnomad4 OTH AF: 0.0531

Alfa AF: 0.0488 Hom.: 20

Bravo AF: 0.0607

Asia WGS AF: 0.0950 AC: 329 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.51
Cadd	Benign	10
Dann	Benign	0.55

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs16212; hg19: chr7-24264661;