16-71600908-A-T

Position:

• chr16-71600908-A-T

Variant summary

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

The XR_933717.2(LOC105371334):​n.239+10866T>A 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 0.685 in 152,044 control chromosomes in the GnomAD database, including 36,028 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 0.69 (36028 hom., cov: 31)
• Consequence: LOC105371334 XR_933717.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.631

Genes affected

LOC105371334 (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 = 0.764 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105371334	XR_933717.2	n.239+10866T>A		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.685 AC: 104125 AN: 151926 Hom.: 35992 Cov.: 31

Gnomad AFR AF: 0.767

Gnomad AMI AF: 0.616

Gnomad AMR AF: 0.701

Gnomad ASJ AF: 0.648

Gnomad EAS AF: 0.784

Gnomad SAS AF: 0.562

Gnomad FIN AF: 0.676

Gnomad MID AF: 0.557

Gnomad NFE AF: 0.639

Gnomad OTH AF: 0.652

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

GnomAD4 genome AF: 0.685 AC: 104217 AN: 152044 Hom.: 36028 Cov.: 31 AF XY: 0.687 AC XY: 51047 AN XY: 74298

Gnomad4 AFR AF: 0.767

Gnomad4 AMR AF: 0.701

Gnomad4 ASJ AF: 0.648

Gnomad4 EAS AF: 0.784

Gnomad4 SAS AF: 0.561

Gnomad4 FIN AF: 0.676

Gnomad4 NFE AF: 0.639

Gnomad4 OTH AF: 0.646

Alfa AF: 0.657 Hom.: 4104

Bravo AF: 0.694

Asia WGS AF: 0.645 AC: 2243 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	3.1
DANN	Benign	0.58

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4788815; hg19: chr16-71634811;