rs13271711

Positions:

• chr8-48451619-C-T

Variant summary

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

The XR_001745891.1(LOC105375821):​n.300-21879C>T 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 0.0396 in 125,116 control chromosomes in the GnomAD database, including 132 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 0.040 (132 hom., cov: 30)
• Consequence: LOC105375821 XR_001745891.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.506

Genes affected

LOC105375821 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.0732 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105375821	XR_001745891.1	n.300-21879C>T		intron_variant, non_coding_transcript_variant
LOC105375821	XR_001745892.1	n.1206-21879C>T		intron_variant, non_coding_transcript_variant
LOC105375821	XR_001745893.1	n.405-21879C>T		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.0396 AC: 4956 AN: 125066 Hom.: 133 Cov.: 30

Gnomad AFR AF: 0.00986

Gnomad AMI AF: 0.106

Gnomad AMR AF: 0.0431

Gnomad ASJ AF: 0.0685

Gnomad EAS AF: 0.00107

Gnomad SAS AF: 0.0810

Gnomad FIN AF: 0.0781

Gnomad MID AF: 0.0913

Gnomad NFE AF: 0.0481

Gnomad OTH AF: 0.0453

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

GnomAD4 genome AF: 0.0396 AC: 4952 AN: 125116 Hom.: 132 Cov.: 30 AF XY: 0.0415 AC XY: 2422 AN XY: 58368

Gnomad4 AFR AF: 0.00984

Gnomad4 AMR AF: 0.0431

Gnomad4 ASJ AF: 0.0685

Gnomad4 EAS AF: 0.00108

Gnomad4 SAS AF: 0.0807

Gnomad4 FIN AF: 0.0781

Gnomad4 NFE AF: 0.0481

Gnomad4 OTH AF: 0.0446

Alfa AF: 0.0395 Hom.: 13

Bravo AF: 0.0303

Asia WGS AF: 0.0260 AC: 90 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.2
DANN	Benign	0.43

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs13271711; hg19: chr8-49364179;