chr16-79379772-C-T

Position:

• chr16-79379772-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.*29-166871G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0224 in 152,142 control chromosomes in the GnomAD database, including 152 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 0.022 (152 hom., cov: 33)
• Consequence: MAF XM_024450279.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.183

Genes affected

MAF (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• 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	Protein	UniProt
MAF	XM_024450279.2	c.*29-166871G>A		intron_variant			XP_024306047.1
MAF	XR_001751902.3	n.2016-166871G>A		intron_variant, non_coding_transcript_variant
MAF	XR_002957802.2	n.2016-166871G>A		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.0223 AC: 3392 AN: 152024 Hom.: 150 Cov.: 33

Gnomad AFR AF: 0.00403

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0519

Gnomad ASJ AF: 0.0225

Gnomad EAS AF: 0.187

Gnomad SAS AF: 0.0659

Gnomad FIN AF: 0.0477

Gnomad MID AF: 0.0127

Gnomad NFE AF: 0.00776

Gnomad OTH AF: 0.0177

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

GnomAD4 genome AF: 0.0224 AC: 3406 AN: 152142 Hom.: 152 Cov.: 33 AF XY: 0.0271 AC XY: 2019 AN XY: 74376

Gnomad4 AFR AF: 0.00402

Gnomad4 AMR AF: 0.0523

Gnomad4 ASJ AF: 0.0225

Gnomad4 EAS AF: 0.187

Gnomad4 SAS AF: 0.0655

Gnomad4 FIN AF: 0.0477

Gnomad4 NFE AF: 0.00776

Gnomad4 OTH AF: 0.0223

Alfa AF: 0.0141 Hom.: 25

Bravo AF: 0.0222

Asia WGS AF: 0.130 AC: 452 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.6
DANN	Benign	0.65

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4390610; hg19: chr16-79413669;