XR_007065161.1:n.4474A>G

Variant names:

• chr16-85980635-T-C
• rs16940202
• XR_007065161.1:n.4474A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XR_007065161.1(LOC124903741):​n.4474A>G 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 0.152 in 152,168 control chromosomes in the GnomAD database, including 2,133 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 0.15 (2133 hom., cov: 32)
• Consequence: LOC124903741 XR_007065161.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0900
• Publications: 34 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=-1.02).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.264 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124903741	XR_007065161.1	n.4474A>G		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+3807A>G		intron_variant	Intron 2 of 2
ENSG00000285040	ENST00000822166.1	n.398-544A>G		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.152 AC: 23139 AN: 152050 Hom.: 2130 Cov.: 32

Gnomad AFR AF: 0.0636

Gnomad AMI AF: 0.322

Gnomad AMR AF: 0.174

Gnomad ASJ AF: 0.319

Gnomad EAS AF: 0.259

Gnomad SAS AF: 0.274

Gnomad FIN AF: 0.146

Gnomad MID AF: 0.274

Gnomad NFE AF: 0.173

Gnomad OTH AF: 0.196

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

GnomAD4 genome AF: 0.152 AC: 23148 AN: 152168 Hom.: 2133 Cov.: 32 AF XY: 0.154 AC XY: 11445 AN XY: 74394

African (AFR) AF: 0.0637 AC: 2642 AN: 41508

American (AMR) AF: 0.174 AC: 2661 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.319 AC: 1106 AN: 3468

East Asian (EAS) AF: 0.259 AC: 1341 AN: 5184

South Asian (SAS) AF: 0.276 AC: 1329 AN: 4818

European-Finnish (FIN) AF: 0.146 AC: 1541 AN: 10590

Middle Eastern (MID) AF: 0.288 AC: 84 AN: 292

European-Non Finnish (NFE) AF: 0.173 AC: 11740 AN: 67996

Other (OTH) AF: 0.194 AC: 410 AN: 2116

Alfa AF: 0.172 Hom.: 8743

Bravo AF: 0.150

Asia WGS AF: 0.255 AC: 885 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.4
DANN	Benign	0.42
PhyloP100		-0.090

Splicing

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

Other links and lift over

dbSNP: rs16940202; hg19: chr16-86014241;