16-86347578-C-G

Variant names:

• chr16-86347578-C-G
• rs11641231
• ENST00000598994.3:n.1705G>C

Variant summary

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

The ENST00000598994.3(LINC00917):​n.1705G>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.203 in 152,424 control chromosomes in the GnomAD database, including 3,354 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 0.20 (3351 hom., cov: 33)
  • Exomes 𝑓: 0.19 (3 hom.)
• Consequence: LINC00917 ENST00000598994.3 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.133
• Publications: 10 publications found

Genes affected

LINC00917 (HGNC:48607): (long intergenic non-protein coding RNA 917)

ENSG00000269826 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.316 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
LINC00917	ENST00000598994.3	n.1705G>C		non_coding_transcript_exon_variant	Exon 2 of 2	2
LINC00917	ENST00000595169.6	n.89+1973G>C		intron_variant	Intron 1 of 5	2
ENSG00000269826	ENST00000595705.1	n.63+129C>G		intron_variant	Intron 1 of 2	3

Frequencies

GnomAD3 genomes AF: 0.203 AC: 30859 AN: 152102 Hom.: 3349 Cov.: 33

Gnomad AFR AF: 0.161

Gnomad AMI AF: 0.185

Gnomad AMR AF: 0.263

Gnomad ASJ AF: 0.174

Gnomad EAS AF: 0.277

Gnomad SAS AF: 0.329

Gnomad FIN AF: 0.130

Gnomad MID AF: 0.256

Gnomad NFE AF: 0.213

Gnomad OTH AF: 0.217

GnomAD4 exome AF: 0.191 AC: 39 AN: 204 Hom.: 3 AF XY: 0.182 AC XY: 27 AN XY: 148

African (AFR) AF: 0.00 AC: 0 AN: 4

American (AMR) AF: 0.500 AC: 2 AN: 4

Ashkenazi Jewish (ASJ) AF: 0.250 AC: 1 AN: 4

East Asian (EAS) AF: 0.00 AC: 0 AN: 2

South Asian (SAS) AF: 0.00 AC: 0 AN: 4

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 6

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.211 AC: 35 AN: 166

Other (OTH) AF: 0.0714 AC: 1 AN: 14

GnomAD4 genome AF: 0.203 AC: 30861 AN: 152220 Hom.: 3351 Cov.: 33 AF XY: 0.204 AC XY: 15163 AN XY: 74430

African (AFR) AF: 0.160 AC: 6661 AN: 41526

American (AMR) AF: 0.263 AC: 4021 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.174 AC: 604 AN: 3470

East Asian (EAS) AF: 0.277 AC: 1431 AN: 5168

South Asian (SAS) AF: 0.330 AC: 1592 AN: 4828

European-Finnish (FIN) AF: 0.130 AC: 1379 AN: 10616

Middle Eastern (MID) AF: 0.248 AC: 73 AN: 294

European-Non Finnish (NFE) AF: 0.213 AC: 14476 AN: 68008

Other (OTH) AF: 0.216 AC: 456 AN: 2112

Alfa AF: 0.114 Hom.: 204

Bravo AF: 0.212

Asia WGS AF: 0.269 AC: 936 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	5.9
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: rs11641231; hg19: chr16-86381184;