chr16-31976404-C-T

Variant names:

• chr16-31976404-C-T
• rs624516

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_Strong BS2

The variant allele was found at a frequency of 0.0065 in 151,490 control chromosomes in the GnomAD database, including 7 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 0.0065 (7 hom., cov: 30)
  • Exomes 𝑓: 0.0056 (28 hom.)
  • Failed GnomAD Quality Control
• Consequence: LOC388248 intragenic
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.140

Genes affected

LOC388248 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -8 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BS2: High Homozygotes in GnomAd4 at 7 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC388248		n.31976404C>T		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000260628	ENST00000568208.6	n.268-105C>T		intron_variant	Intron 2 of 14	6

Frequencies

GnomAD3 genomes AF: 0.00649 AC: 983 AN: 151374 Hom.: 7 Cov.: 30

Gnomad AFR AF: 0.00362

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0110

Gnomad ASJ AF: 0.0110

Gnomad EAS AF: 0.000973

Gnomad SAS AF: 0.00498

Gnomad FIN AF: 0.000282

Gnomad MID AF: 0.0223

Gnomad NFE AF: 0.00824

Gnomad OTH AF: 0.0144

GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.00558 AC: 3775 AN: 676828 Hom.: 28 AF XY: 0.00587 AC XY: 2058 AN XY: 350648

Gnomad4 AFR exome AF: 0.00247

Gnomad4 AMR exome AF: 0.00670

Gnomad4 ASJ exome AF: 0.00842

Gnomad4 EAS exome AF: 0.00183

Gnomad4 SAS exome AF: 0.00687

Gnomad4 FIN exome AF: 0.000195

Gnomad4 NFE exome AF: 0.00598

Gnomad4 OTH exome AF: 0.00761

GnomAD4 genome AF: 0.00650 AC: 984 AN: 151490 Hom.: 7 Cov.: 30 AF XY: 0.00627 AC XY: 464 AN XY: 74050

Gnomad4 AFR AF: 0.00361

Gnomad4 AMR AF: 0.0110

Gnomad4 ASJ AF: 0.0110

Gnomad4 EAS AF: 0.000975

Gnomad4 SAS AF: 0.00499

Gnomad4 FIN AF: 0.000282

Gnomad4 NFE AF: 0.00824

Gnomad4 OTH AF: 0.0143

Alfa AF: 0.00539 Hom.: 0

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	5.4
DANN	Benign	0.66

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs624516; hg19: chr16-31987725;