rs4128452

Positions:

• chr16-79368240-T-C
• chr16-79368240-T-G

Variant summary

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

The XM_024450279.2(MAF):​c.*29-155339A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0434 in 152,186 control chromosomes in the GnomAD database, including 279 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 0.043 (279 hom., cov: 32)
• Consequence: MAF XM_024450279.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.253

Genes affected

MAF (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.185 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MAF	XM_024450279.2	c.*29-155339A>G		intron_variant			XP_024306047.1
MAF	XR_001751902.3	n.2016-155339A>G		intron_variant, non_coding_transcript_variant
MAF	XR_002957802.2	n.2016-155339A>G		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.0432 AC: 6576 AN: 152068 Hom.: 277 Cov.: 32

Gnomad AFR AF: 0.0755

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0597

Gnomad ASJ AF: 0.0222

Gnomad EAS AF: 0.195

Gnomad SAS AF: 0.0691

Gnomad FIN AF: 0.0478

Gnomad MID AF: 0.0127

Gnomad NFE AF: 0.00810

Gnomad OTH AF: 0.0306

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

GnomAD4 genome AF: 0.0434 AC: 6603 AN: 152186 Hom.: 279 Cov.: 32 AF XY: 0.0482 AC XY: 3582 AN XY: 74380

Gnomad4 AFR AF: 0.0756

Gnomad4 AMR AF: 0.0601

Gnomad4 ASJ AF: 0.0222

Gnomad4 EAS AF: 0.195

Gnomad4 SAS AF: 0.0687

Gnomad4 FIN AF: 0.0478

Gnomad4 NFE AF: 0.00810

Gnomad4 OTH AF: 0.0355

Alfa AF: 0.00870 Hom.: 1

Bravo AF: 0.0465

Asia WGS AF: 0.144 AC: 499 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.1
DANN	Benign	0.53

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4128452; hg19: chr16-79402137;