6-79844864-G-T

Variant names:

• chr6-79844864-G-T
• rs719172
• ENST00000784459.1:n.386+33300C>A

Variant summary

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

The ENST00000784459.1(LINC01621):​n.386+33300C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.14 in 152,084 control chromosomes in the GnomAD database, including 1,920 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 0.14 (1920 hom., cov: 30)
• Consequence: LINC01621 ENST00000784459.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.125
• Publications: 3 publications found

Genes affected

LINC01621 (HGNC:14109): (long intergenic non-protein coding RNA 1621)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.414 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01621	ENST00000784459.1	n.386+33300C>A		intron_variant	Intron 1 of 3
LINC01621	ENST00000784460.1	n.700+20594C>A		intron_variant	Intron 3 of 5

Frequencies

GnomAD3 genomes AF: 0.140 AC: 21324 AN: 151964 Hom.: 1915 Cov.: 30

Gnomad AFR AF: 0.178

Gnomad AMI AF: 0.0274

Gnomad AMR AF: 0.181

Gnomad ASJ AF: 0.127

Gnomad EAS AF: 0.428

Gnomad SAS AF: 0.191

Gnomad FIN AF: 0.0966

Gnomad MID AF: 0.0823

Gnomad NFE AF: 0.0924

Gnomad OTH AF: 0.128

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

GnomAD4 genome AF: 0.140 AC: 21358 AN: 152084 Hom.: 1920 Cov.: 30 AF XY: 0.144 AC XY: 10679 AN XY: 74360

African (AFR) AF: 0.178 AC: 7389 AN: 41478

American (AMR) AF: 0.182 AC: 2779 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.127 AC: 440 AN: 3470

East Asian (EAS) AF: 0.428 AC: 2204 AN: 5144

South Asian (SAS) AF: 0.190 AC: 915 AN: 4814

European-Finnish (FIN) AF: 0.0966 AC: 1024 AN: 10598

Middle Eastern (MID) AF: 0.0748 AC: 22 AN: 294

European-Non Finnish (NFE) AF: 0.0924 AC: 6283 AN: 67996

Other (OTH) AF: 0.131 AC: 277 AN: 2108

Alfa AF: 0.103 Hom.: 441

Bravo AF: 0.149

Asia WGS AF: 0.320 AC: 1110 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	4.4
DANN	Benign	0.54
PhyloP100		0.13

Splicing

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

Other links and lift over

dbSNP: rs719172; hg19: chr6-80554581;