XR_007065161.1:n.7378G>A

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 27 publications found

Genes affected

LOC124903741 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000645754.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000285040	ENST00000645754.1		n.227+6711G>A		intron	N/A
	ENSG00000294410	ENST00000723428.1		n.*97C>T		downstream_gene	N/A

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

African (AFR) AF: 0.0133 AC: 551 AN: 41546

American (AMR) AF: 0.0282 AC: 431 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.0265 AC: 92 AN: 3470

East Asian (EAS) AF: 0.0788 AC: 408 AN: 5180

South Asian (SAS) AF: 0.0581 AC: 280 AN: 4818

European-Finnish (FIN) AF: 0.134 AC: 1418 AN: 10566

Middle Eastern (MID) AF: 0.0374 AC: 11 AN: 294

European-Non Finnish (NFE) AF: 0.0951 AC: 6463 AN: 67988

Other (OTH) AF: 0.0459 AC: 97 AN: 2112

Alfa AF: 0.0780 Hom.: 1742

Bravo AF: 0.0527

Asia WGS AF: 0.0710 AC: 248 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.93
DANN	Benign	0.74
PhyloP100		-2.5

Splicing

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

Other links and lift over

dbSNP: rs10521318; hg19: chr16-86011337;