16-86331965-C-G

Variant names:

• chr16-86331965-C-G
• rs2696835
• ENST00000594203.5:n.2557G>C

Variant summary

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

The ENST00000594203.5(LINC00917):​n.2557G>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 0.982 in 152,366 control chromosomes in the GnomAD database, including 73,529 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 0.98 (73521 hom., cov: 32)
  • Exomes 𝑓: 1.0 (8 hom.)
• Consequence: LINC00917 ENST00000594203.5 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.122
• Publications: 10 publications found

Genes affected

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

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.987 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC00917	NR_024406.1	n.2503G>C		non_coding_transcript_exon_variant	Exon 7 of 7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC00917	ENST00000594203.5	n.2557G>C		non_coding_transcript_exon_variant	Exon 6 of 6	1
LINC00917	ENST00000600892.5	n.1411G>C		non_coding_transcript_exon_variant	Exon 5 of 5	1
LINC00917	ENST00000595169.6	n.2318G>C		non_coding_transcript_exon_variant	Exon 6 of 6	2

Frequencies

GnomAD3 genomes AF: 0.982 AC: 149551 AN: 152232 Hom.: 73464 Cov.: 32

Gnomad AFR AF: 0.995

Gnomad AMI AF: 0.975

Gnomad AMR AF: 0.987

Gnomad ASJ AF: 0.979

Gnomad EAS AF: 1.00

Gnomad SAS AF: 0.983

Gnomad FIN AF: 0.980

Gnomad MID AF: 0.975

Gnomad NFE AF: 0.973

Gnomad OTH AF: 0.982

GnomAD4 exome AF: 1.00 AC: 16 AN: 16 Hom.: 8 Cov.: 0 AF XY: 1.00 AC XY: 12 AN XY: 12

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 1.00 AC: 4 AN: 4

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 1.00 AC: 12 AN: 12

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.982 AC: 149667 AN: 152350 Hom.: 73521 Cov.: 32 AF XY: 0.984 AC XY: 73270 AN XY: 74498

African (AFR) AF: 0.995 AC: 41376 AN: 41572

American (AMR) AF: 0.987 AC: 15108 AN: 15312

Ashkenazi Jewish (ASJ) AF: 0.979 AC: 3400 AN: 3472

East Asian (EAS) AF: 1.00 AC: 5179 AN: 5180

South Asian (SAS) AF: 0.983 AC: 4740 AN: 4824

European-Finnish (FIN) AF: 0.980 AC: 10414 AN: 10626

Middle Eastern (MID) AF: 0.969 AC: 285 AN: 294

European-Non Finnish (NFE) AF: 0.973 AC: 66197 AN: 68042

Other (OTH) AF: 0.983 AC: 2079 AN: 2116

Alfa AF: 0.976 Hom.: 40130

Bravo AF: 0.983

Asia WGS AF: 0.993 AC: 3453 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.88
DANN	Benign	0.66
PhyloP100		-0.12

Splicing

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

Other links and lift over

dbSNP: rs2696835; hg19: chr16-86365571;