chr2-19869619-C-A

Variant names:

• chr2-19869619-C-A
• rs2276607
• ENST00000449086.5:n.197+6C>A

Variant summary

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

The ENST00000449086.5(LINC00954):​n.197+6C>A variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.184 in 152,362 control chromosomes in the GnomAD database, including 2,894 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 0.18 (2890 hom., cov: 33)
  • Exomes 𝑓: 0.19 (4 hom.)
• Consequence: LINC00954 ENST00000449086.5 splice_region, intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.640
• Publications: 7 publications found

Genes affected

LINC00954 (HGNC:48668): (long intergenic non-protein coding RNA 954)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.286 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000449086.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC00954	NR_033875.1		n.217+6C>A		splice_region intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC00954	ENST00000449086.5	TSL:1	n.197+6C>A		splice_region intron	N/A
	LINC00954	ENST00000760064.1		n.1519C>A		non_coding_transcript_exon	Exon 2 of 2
	LINC00954	ENST00000760068.1		n.312C>A		non_coding_transcript_exon	Exon 2 of 2

Frequencies

GnomAD3 genomes AF: 0.183 AC: 27901 AN: 152072 Hom.: 2887 Cov.: 33

Gnomad AFR AF: 0.264

Gnomad AMI AF: 0.120

Gnomad AMR AF: 0.200

Gnomad ASJ AF: 0.0979

Gnomad EAS AF: 0.299

Gnomad SAS AF: 0.254

Gnomad FIN AF: 0.112

Gnomad MID AF: 0.120

Gnomad NFE AF: 0.133

Gnomad OTH AF: 0.182

GnomAD4 exome AF: 0.192 AC: 33 AN: 172 Hom.: 4 Cov.: 0 AF XY: 0.216 AC XY: 29 AN XY: 134

African (AFR) AC: 0 AN: 0

American (AMR) AF: 0.00 AC: 0 AN: 2

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 4

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AF: 0.500 AC: 1 AN: 2

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 4

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.194 AC: 28 AN: 144

Other (OTH) AF: 0.250 AC: 4 AN: 16

GnomAD4 genome AF: 0.184 AC: 27929 AN: 152190 Hom.: 2890 Cov.: 33 AF XY: 0.184 AC XY: 13719 AN XY: 74406

African (AFR) AF: 0.264 AC: 10958 AN: 41522

American (AMR) AF: 0.200 AC: 3065 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.0979 AC: 340 AN: 3472

East Asian (EAS) AF: 0.299 AC: 1544 AN: 5166

South Asian (SAS) AF: 0.255 AC: 1228 AN: 4824

European-Finnish (FIN) AF: 0.112 AC: 1188 AN: 10598

Middle Eastern (MID) AF: 0.126 AC: 37 AN: 294

European-Non Finnish (NFE) AF: 0.133 AC: 9069 AN: 67992

Other (OTH) AF: 0.185 AC: 391 AN: 2112

Alfa AF: 0.148 Hom.: 3050

Bravo AF: 0.194

Asia WGS AF: 0.301 AC: 1047 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	1.1
DANN	Benign	0.35
PhyloP100		-0.64

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs2276607;

hg19: chr2-20069380;