rs7038156

Variant names:

• chr9-94197133-A-G
• rs7038156
• ENST00000416309.6:n.164+2065T>C

Variant summary

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

The ENST00000416309.6(LINC02603):​n.164+2065T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.192 in 152,064 control chromosomes in the GnomAD database, including 3,097 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 0.19 (3097 hom., cov: 32)
• Consequence: LINC02603 ENST00000416309.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.258
• Publications: 2 publications found

Genes affected

LINC02603 (HGNC:37186): (long intergenic non-protein coding RNA 2603)

MIRLET7A1HG (HGNC:53970): (miRlet-7a-1/let-7f-1/let-7d cluster host gene)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.273 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC02603	NR_046163.1	n.187+2065T>C		intron_variant	Intron 3 of 3
LINC02603	NR_046165.1	n.128+2065T>C		intron_variant	Intron 2 of 2
LINC02603	NR_160773.1	n.255+2065T>C		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02603	ENST00000416309.6	n.164+2065T>C		intron_variant	Intron 3 of 3	1
LINC02603	ENST00000602602.3	n.158+2065T>C		intron_variant	Intron 2 of 2	1
LINC02603	ENST00000602652.3	n.408+2065T>C		intron_variant	Intron 3 of 3	6

Frequencies

GnomAD3 genomes AF: 0.192 AC: 29228 AN: 151946 Hom.: 3094 Cov.: 32

Gnomad AFR AF: 0.277

Gnomad AMI AF: 0.0692

Gnomad AMR AF: 0.136

Gnomad ASJ AF: 0.154

Gnomad EAS AF: 0.0193

Gnomad SAS AF: 0.131

Gnomad FIN AF: 0.205

Gnomad MID AF: 0.196

Gnomad NFE AF: 0.173

Gnomad OTH AF: 0.170

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

GnomAD4 genome AF: 0.192 AC: 29253 AN: 152064 Hom.: 3097 Cov.: 32 AF XY: 0.190 AC XY: 14130 AN XY: 74334

African (AFR) AF: 0.277 AC: 11491 AN: 41452

American (AMR) AF: 0.136 AC: 2073 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.154 AC: 535 AN: 3470

East Asian (EAS) AF: 0.0193 AC: 100 AN: 5174

South Asian (SAS) AF: 0.131 AC: 630 AN: 4816

European-Finnish (FIN) AF: 0.205 AC: 2169 AN: 10592

Middle Eastern (MID) AF: 0.211 AC: 62 AN: 294

European-Non Finnish (NFE) AF: 0.173 AC: 11776 AN: 67974

Other (OTH) AF: 0.168 AC: 354 AN: 2108

Alfa AF: 0.173 Hom.: 3155

Bravo AF: 0.189

Asia WGS AF: 0.111 AC: 388 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	4.9
DANN	Benign	0.82
PhyloP100		0.26

Splicing

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

Other links and lift over

dbSNP: rs7038156; hg19: chr9-96959415;