rs631208

chr16-9305867-A-G

Variant summary

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

The XR_007064980.1(LOC101927026):n.72+121134A>G 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 0.407 in 151,938 control chromosomes in the GnomAD database, including 12,905 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 0.41 (12905 hom., cov: 31)
• Consequence: LOC101927026 XR_007064980.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.465

Genes affected

LOC101927026 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.447 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC101927026	XR_007064980.1	n.72+121134A>G		intron_variant, non_coding_transcript_variant
LOC101927026	XR_933053.3	n.80+18615A>G		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.407 AC: 61849 AN: 151820 Hom.: 12893 Cov.: 31

Gnomad AFR AF: 0.452

Gnomad AMI AF: 0.234

Gnomad AMR AF: 0.364

Gnomad ASJ AF: 0.424

Gnomad EAS AF: 0.278

Gnomad SAS AF: 0.374

Gnomad FIN AF: 0.379

Gnomad MID AF: 0.377

Gnomad NFE AF: 0.408

Gnomad OTH AF: 0.408

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

GnomAD4 genome AF: 0.407 AC: 61891 AN: 151938 Hom.: 12905 Cov.: 31 AF XY: 0.405 AC XY: 30093 AN XY: 74256

Gnomad4 AFR AF: 0.452

Gnomad4 AMR AF: 0.363

Gnomad4 ASJ AF: 0.424

Gnomad4 EAS AF: 0.279

Gnomad4 SAS AF: 0.375

Gnomad4 FIN AF: 0.379

Gnomad4 NFE AF: 0.408

Gnomad4 OTH AF: 0.405

Alfa AF: 0.402 Hom.: 27847

Bravo AF: 0.405

Asia WGS AF: 0.342 AC: 1189 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	0.29

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs631208; hg19: chr16-9399724;