rs6498486

Variant names:

• chr16-13919809-A-C
• rs6498486
• XR_007065001.1:n.270T>G

Your query was ambiguous. Multiple possible variants found:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 41 publications found

Genes affected

LOC124903647 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 VariationId 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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.286 AC: 11840 AN: 41466

American (AMR) AF: 0.258 AC: 3952 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.286 AC: 992 AN: 3468

East Asian (EAS) AF: 0.258 AC: 1336 AN: 5170

South Asian (SAS) AF: 0.294 AC: 1418 AN: 4822

European-Finnish (FIN) AF: 0.231 AC: 2439 AN: 10568

Middle Eastern (MID) AF: 0.340 AC: 100 AN: 294

European-Non Finnish (NFE) AF: 0.276 AC: 18768 AN: 67988

Other (OTH) AF: 0.298 AC: 628 AN: 2108

Alfa AF: 0.241 Hom.: 1344

Bravo AF: 0.276

ClinVar

ClinVar submissions

Significance: Benign

Revision: criteria provided, single submitter

Pathogenic	VUS	Benign	Condition
-	-	1	Cockayne syndrome;C0268140:Xeroderma pigmentosum, group F;C3808988:Fanconi anemia complementation group Q (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	0.20
DANN	Benign	0.45
PhyloP100		-2.9
PromoterAI		-0.070	Neutral

Splicing

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

Other links and lift over

dbSNP: rs6498486; hg19: chr16-14013666;