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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124903647	XR_007065001.1	n.270T>G		non_coding_transcript_exon_variant	Exon 1 of 2
LOC105371093	XR_007064999.1	n.82+6716T>G		intron_variant	Intron 1 of 2
LOC105371093	XR_007065000.1	n.82+6716T>G		intron_variant	Intron 1 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

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

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

Jan 23, 2025

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

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Computational scores

Source: dbNSFP v4.3

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;