chr16-85977731-C-T

Variant names:

• chr16-85977731-C-T
• rs10521318
• XR_007065161.1:n.7378G>A

Variant summary

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

The XR_007065161.1(LOC124903741):​n.7378G>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0643 in 152,162 control chromosomes in the GnomAD database, including 462 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 0.064 (462 hom., cov: 33)
• Consequence: LOC124903741 XR_007065161.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.53

Genes affected

LOC124903741 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0931 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124903741	XR_007065161.1	n.7378G>A		non_coding_transcript_exon_variant	Exon 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000285040	ENST00000645754.1	n.227+6711G>A		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.0644 AC: 9789 AN: 152044 Hom.: 462 Cov.: 33

Gnomad AFR AF: 0.0133

Gnomad AMI AF: 0.0373

Gnomad AMR AF: 0.0284

Gnomad ASJ AF: 0.0265

Gnomad EAS AF: 0.0786

Gnomad SAS AF: 0.0583

Gnomad FIN AF: 0.134

Gnomad MID AF: 0.0380

Gnomad NFE AF: 0.0950

Gnomad OTH AF: 0.0464

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

GnomAD4 genome AF: 0.0643 AC: 9785 AN: 152162 Hom.: 462 Cov.: 33 AF XY: 0.0656 AC XY: 4880 AN XY: 74394

Gnomad4 AFR AF: 0.0133

Gnomad4 AMR AF: 0.0282

Gnomad4 ASJ AF: 0.0265

Gnomad4 EAS AF: 0.0788

Gnomad4 SAS AF: 0.0581

Gnomad4 FIN AF: 0.134

Gnomad4 NFE AF: 0.0951

Gnomad4 OTH AF: 0.0459

Alfa AF: 0.0777 Hom.: 709

Bravo AF: 0.0527

Asia WGS AF: 0.0710 AC: 248 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.93
DANN	Benign	0.74

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10521318; hg19: chr16-86011337;