rs6693882

Variant names:

• chr1-95680412-A-G
• rs6693882
• ENST00000456933.1:n.308-96735A>G

Your query was ambiguous. Multiple possible variants found:

• chr1-95680412-A-G
• chr1-95680412-A-T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000456933.1(LINC02607):​n.308-96735A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.375 in 152,102 control chromosomes in the GnomAD database, including 13,266 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 0.38 (13266 hom., cov: 32)
• Consequence: LINC02607 ENST00000456933.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.163
• Publications: 12 publications found

Genes affected

LINC02607 (HGNC:54049): (long intergenic non-protein coding RNA 2607)

LOC101928219 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.521 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC101928219	XR_001738162.2	n.133+54847A>G		intron_variant	Intron 1 of 3
LOC101928219	XR_246378.6	n.133+54847A>G		intron_variant	Intron 1 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02607	ENST00000456933.1	n.308-96735A>G		intron_variant	Intron 2 of 3	3
LINC02607	ENST00000664663.1	n.133+54847A>G		intron_variant	Intron 1 of 1
LINC02607	ENST00000665349.1	n.160+54768A>G		intron_variant	Intron 1 of 2
LINC02607	ENST00000819547.1	n.304+1218A>G		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.376 AC: 57072 AN: 151984 Hom.: 13270 Cov.: 32

Gnomad AFR AF: 0.112

Gnomad AMI AF: 0.319

Gnomad AMR AF: 0.361

Gnomad ASJ AF: 0.460

Gnomad EAS AF: 0.233

Gnomad SAS AF: 0.538

Gnomad FIN AF: 0.471

Gnomad MID AF: 0.481

Gnomad NFE AF: 0.520

Gnomad OTH AF: 0.392

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

GnomAD4 genome AF: 0.375 AC: 57066 AN: 152102 Hom.: 13266 Cov.: 32 AF XY: 0.373 AC XY: 27694 AN XY: 74344

African (AFR) AF: 0.111 AC: 4624 AN: 41550

American (AMR) AF: 0.360 AC: 5492 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.460 AC: 1597 AN: 3468

East Asian (EAS) AF: 0.233 AC: 1205 AN: 5166

South Asian (SAS) AF: 0.539 AC: 2594 AN: 4816

European-Finnish (FIN) AF: 0.471 AC: 4974 AN: 10562

Middle Eastern (MID) AF: 0.473 AC: 139 AN: 294

European-Non Finnish (NFE) AF: 0.520 AC: 35317 AN: 67958

Other (OTH) AF: 0.395 AC: 833 AN: 2108

Alfa AF: 0.455 Hom.: 53851

Bravo AF: 0.351

Asia WGS AF: 0.361 AC: 1258 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.7
DANN	Benign	0.39
PhyloP100		0.16

Splicing

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

Other links and lift over

dbSNP: rs6693882; hg19: chr1-96145968;