16-79373021-C-T

Position:

• chr16-79373021-C-T

Variant summary

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

The XM_024450279.2(MAF):​c.*29-160120G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0419 in 152,144 control chromosomes in the GnomAD database, including 264 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 0.042 (264 hom., cov: 31)
• Consequence: MAF XM_024450279.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -4.10

Genes affected

MAF (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.177 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MAF	XM_024450279.2	c.*29-160120G>A		intron_variant
MAF	XR_001751902.3	n.2016-160120G>A		intron_variant, non_coding_transcript_variant
MAF	XR_002957802.2	n.2016-160120G>A		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.0418 AC: 6356 AN: 152026 Hom.: 262 Cov.: 31

Gnomad AFR AF: 0.0722

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0591

Gnomad ASJ AF: 0.0222

Gnomad EAS AF: 0.186

Gnomad SAS AF: 0.0652

Gnomad FIN AF: 0.0476

Gnomad MID AF: 0.0127

Gnomad NFE AF: 0.00803

Gnomad OTH AF: 0.0287

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

GnomAD4 genome AF: 0.0419 AC: 6380 AN: 152144 Hom.: 264 Cov.: 31 AF XY: 0.0468 AC XY: 3477 AN XY: 74370

Gnomad4 AFR AF: 0.0723

Gnomad4 AMR AF: 0.0595

Gnomad4 ASJ AF: 0.0222

Gnomad4 EAS AF: 0.186

Gnomad4 SAS AF: 0.0648

Gnomad4 FIN AF: 0.0476

Gnomad4 NFE AF: 0.00803

Gnomad4 OTH AF: 0.0331

Alfa AF: 0.0166 Hom.: 107

Bravo AF: 0.0449

Asia WGS AF: 0.133 AC: 461 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.098
DANN	Benign	0.37

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17797882; hg19: chr16-79406918;