rs208679

chr11-34432514-A-G

Variant summary

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

The XR_931180.3(LOC105376622):n.159+67A>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 0.0941 in 152,242 control chromosomes in the GnomAD database, including 862 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 0.094 (862 hom., cov: 32)
• Consequence: LOC105376622 XR_931180.3 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.612

Genes affected

LOC105376622 (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 (EAS) allele frequency at 95% confidence interval = 0.221 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105376622	XR_931180.3	n.159+67A>G		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.0940 AC: 14304 AN: 152124 Hom.: 856 Cov.: 32

Gnomad AFR AF: 0.109

Gnomad AMI AF: 0.00441

Gnomad AMR AF: 0.132

Gnomad ASJ AF: 0.0685

Gnomad EAS AF: 0.233

Gnomad SAS AF: 0.121

Gnomad FIN AF: 0.113

Gnomad MID AF: 0.0380

Gnomad NFE AF: 0.0641

Gnomad OTH AF: 0.0832

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

GnomAD4 genome AF: 0.0941 AC: 14325 AN: 152242 Hom.: 862 Cov.: 32 AF XY: 0.0970 AC XY: 7219 AN XY: 74432

Gnomad4 AFR AF: 0.109

Gnomad4 AMR AF: 0.133

Gnomad4 ASJ AF: 0.0685

Gnomad4 EAS AF: 0.232

Gnomad4 SAS AF: 0.121

Gnomad4 FIN AF: 0.113

Gnomad4 NFE AF: 0.0641

Gnomad4 OTH AF: 0.0856

Alfa AF: 0.0661 Hom.: 392

Bravo AF: 0.0963

Asia WGS AF: 0.182 AC: 631 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	3.2
Dann	Benign	0.67

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs208679; hg19: chr11-34454061;