rs6943606

Variant names:

• chr7-25786929-C-A
• rs6943606
• ENST00000812174.1:n.297+61997G>T

Your query was ambiguous. Multiple possible variants found:

• chr7-25786929-C-A
• chr7-25786929-C-G

Variant summary

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

The ENST00000812174.1(ENSG00000286725):​n.297+61997G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0632 in 152,272 control chromosomes in the GnomAD database, including 575 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 0.063 (575 hom., cov: 33)
• Consequence: ENSG00000286725 ENST00000812174.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.325
• Publications: 5 publications found

Genes affected

ENSG00000286725 (HGNC:):

LINC03007 (HGNC:56132): (long intergenic non-protein coding RNA 3007)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.141 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC03007	NR_157808.1	n.367+2824G>T		intron_variant	Intron 1 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000286725	ENST00000812174.1	n.297+61997G>T		intron_variant	Intron 2 of 4
ENSG00000286725	ENST00000812175.1	n.280+61997G>T		intron_variant	Intron 2 of 5
ENSG00000286725	ENST00000812176.1	n.297+61997G>T		intron_variant	Intron 2 of 4
ENSG00000286725	ENST00000812177.1	n.280+61997G>T		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.0631 AC: 9608 AN: 152154 Hom.: 572 Cov.: 33

Gnomad AFR AF: 0.144

Gnomad AMI AF: 0.00987

Gnomad AMR AF: 0.0891

Gnomad ASJ AF: 0.0132

Gnomad EAS AF: 0.131

Gnomad SAS AF: 0.0455

Gnomad FIN AF: 0.00613

Gnomad MID AF: 0.0633

Gnomad NFE AF: 0.0165

Gnomad OTH AF: 0.0569

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

GnomAD4 genome AF: 0.0632 AC: 9623 AN: 152272 Hom.: 575 Cov.: 33 AF XY: 0.0618 AC XY: 4605 AN XY: 74456

African (AFR) AF: 0.144 AC: 5974 AN: 41536

American (AMR) AF: 0.0894 AC: 1367 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.0132 AC: 46 AN: 3472

East Asian (EAS) AF: 0.131 AC: 679 AN: 5188

South Asian (SAS) AF: 0.0456 AC: 220 AN: 4826

European-Finnish (FIN) AF: 0.00613 AC: 65 AN: 10612

Middle Eastern (MID) AF: 0.0544 AC: 16 AN: 294

European-Non Finnish (NFE) AF: 0.0165 AC: 1123 AN: 68030

Other (OTH) AF: 0.0587 AC: 124 AN: 2112

Alfa AF: 0.0291 Hom.: 254

Bravo AF: 0.0770

Asia WGS AF: 0.115 AC: 400 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	6.0
DANN	Benign	0.38
PhyloP100		0.33

Splicing

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

Other links and lift over

dbSNP: rs6943606; hg19: chr7-25826549;