rs6498486

Positions:

• chr16-13919809-A-C
• chr16-13919809-A-T

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The XR_007065001.1(LOC124903647):​n.270T>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 0.275 in 152,088 control chromosomes in the GnomAD database, including 5,831 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.27 (5831 hom., cov: 33)
• Consequence: LOC124903647 XR_007065001.1 non_coding_transcript_exon
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -2.92

Genes affected

LOC124903647 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BP6: Variant 16-13919809-A-C is Benign according to our data. Variant chr16-13919809-A-C is described in ClinVar as [Benign]. Clinvar id is 1164457.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.281 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC124903647	XR_007065001.1	n.270T>G		non_coding_transcript_exon_variant	1/2
LOC105371093	XR_007065000.1	n.82+6716T>G		intron_variant, non_coding_transcript_variant
LOC105371093	XR_007064999.1	n.82+6716T>G		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.274 AC: 41703 AN: 151970 Hom.: 5821 Cov.: 33

Gnomad AFR AF: 0.285

Gnomad AMI AF: 0.314

Gnomad AMR AF: 0.258

Gnomad ASJ AF: 0.286

Gnomad EAS AF: 0.259

Gnomad SAS AF: 0.292

Gnomad FIN AF: 0.231

Gnomad MID AF: 0.342

Gnomad NFE AF: 0.276

Gnomad OTH AF: 0.296

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

GnomAD4 genome AF: 0.275 AC: 41759 AN: 152088 Hom.: 5831 Cov.: 33 AF XY: 0.272 AC XY: 20239 AN XY: 74338

Gnomad4 AFR AF: 0.286

Gnomad4 AMR AF: 0.258

Gnomad4 ASJ AF: 0.286

Gnomad4 EAS AF: 0.258

Gnomad4 SAS AF: 0.294

Gnomad4 FIN AF: 0.231

Gnomad4 NFE AF: 0.276

Gnomad4 OTH AF: 0.298

Alfa AF: 0.210 Hom.: 701

Bravo AF: 0.276

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

Cockayne syndrome;C0268140:Xeroderma pigmentosum, group F;C3808988:Fanconi anemia complementation group Q Benign:1

Benign, criteria provided, single submitter

clinical testing

Invitae

Jul 17, 2023

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	0.20
DANN	Benign	0.45

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6498486; hg19: chr16-14013666;