rs6693882

Positions:

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

Variant summary

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

The ENST00000456933.1(LINC02607):​n.308-96735A>G 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 0.375 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, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.163

Genes affected

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

LOC101928219 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt
LOC101928219	XR_001738162.2	n.133+54847A>G		intron_variant, non_coding_transcript_variant
LOC101928219	XR_246378.6	n.133+54847A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC02607	ENST00000456933.1	n.308-96735A>G		intron_variant, non_coding_transcript_variant		3
LINC02607	ENST00000664663.1	n.133+54847A>G		intron_variant, non_coding_transcript_variant
LINC02607	ENST00000665349.1	n.160+54768A>G		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.111

Gnomad4 AMR AF: 0.360

Gnomad4 ASJ AF: 0.460

Gnomad4 EAS AF: 0.233

Gnomad4 SAS AF: 0.539

Gnomad4 FIN AF: 0.471

Gnomad4 NFE AF: 0.520

Gnomad4 OTH AF: 0.395

Alfa AF: 0.479 Hom.: 34556

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6693882; hg19: chr1-96145968;