rs6696854

Positions:

• chr1-161494024-T-C

Variant summary

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

The XR_922214.3(LOC105371473):​n.1903+405T>C 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 0.738 in 152,012 control chromosomes in the GnomAD database, including 42,187 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 0.74 (42187 hom., cov: 31)
• Consequence: LOC105371473 XR_922214.3 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.20

Genes affected

LOC105371473 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.762 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105371473	XR_922214.3	n.1903+405T>C		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.738 AC: 112043 AN: 151894 Hom.: 42160 Cov.: 31

Gnomad AFR AF: 0.754

Gnomad AMI AF: 0.739

Gnomad AMR AF: 0.770

Gnomad ASJ AF: 0.809

Gnomad EAS AF: 0.283

Gnomad SAS AF: 0.541

Gnomad FIN AF: 0.724

Gnomad MID AF: 0.801

Gnomad NFE AF: 0.767

Gnomad OTH AF: 0.733

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

GnomAD4 genome AF: 0.738 AC: 112127 AN: 152012 Hom.: 42187 Cov.: 31 AF XY: 0.732 AC XY: 54393 AN XY: 74296

Gnomad4 AFR AF: 0.755

Gnomad4 AMR AF: 0.769

Gnomad4 ASJ AF: 0.809

Gnomad4 EAS AF: 0.284

Gnomad4 SAS AF: 0.540

Gnomad4 FIN AF: 0.724

Gnomad4 NFE AF: 0.767

Gnomad4 OTH AF: 0.730

Alfa AF: 0.760 Hom.: 91462

Bravo AF: 0.746

Asia WGS AF: 0.454 AC: 1585 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	0.17
DANN	Benign	0.14

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6696854; hg19: chr1-161463814;