rs10499196

Variant names:

• chr6-137698529-C-A
• rs10499196
• ENST00000793597.1:n.1305G>T

Variant summary

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

The ENST00000793597.1(ENSG00000303318):​n.1305G>T 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 0.09 in 151,800 control chromosomes in the GnomAD database, including 675 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 0.090 (675 hom., cov: 31)
  • Exomes 𝑓: 0.12 (0 hom.)
• Consequence: ENSG00000303318 ENST00000793597.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.579
• Publications: 7 publications found

Genes affected

ENSG00000303318 (HGNC:):

LINC03004 (HGNC:56128): (long intergenic non-protein coding RNA 3004)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.156 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000793597.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000303318	ENST00000793597.1		n.1305G>T		non_coding_transcript_exon	Exon 3 of 3
	ENSG00000303318	ENST00000793599.1		n.1290G>T		non_coding_transcript_exon	Exon 2 of 2
	ENSG00000303318	ENST00000793600.1		n.1111G>T		non_coding_transcript_exon	Exon 2 of 2

Frequencies

GnomAD3 genomes AF: 0.0900 AC: 13635 AN: 151532 Hom.: 671 Cov.: 31

Gnomad AFR AF: 0.0601

Gnomad AMI AF: 0.119

Gnomad AMR AF: 0.0749

Gnomad ASJ AF: 0.117

Gnomad EAS AF: 0.165

Gnomad SAS AF: 0.132

Gnomad FIN AF: 0.102

Gnomad MID AF: 0.139

Gnomad NFE AF: 0.0990

Gnomad OTH AF: 0.0882

GnomAD4 exome AF: 0.122 AC: 19 AN: 156 Hom.: 0 AF XY: 0.0978 AC XY: 9 AN XY: 92

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AF: 0.116 AC: 16 AN: 138

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.500 AC: 1 AN: 2

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.0833 AC: 1 AN: 12

Other (OTH) AF: 0.250 AC: 1 AN: 4

GnomAD4 genome AF: 0.0900 AC: 13650 AN: 151644 Hom.: 675 Cov.: 31 AF XY: 0.0909 AC XY: 6729 AN XY: 74052

African (AFR) AF: 0.0600 AC: 2481 AN: 41336

American (AMR) AF: 0.0755 AC: 1150 AN: 15240

Ashkenazi Jewish (ASJ) AF: 0.117 AC: 407 AN: 3468

East Asian (EAS) AF: 0.165 AC: 852 AN: 5158

South Asian (SAS) AF: 0.134 AC: 639 AN: 4786

European-Finnish (FIN) AF: 0.102 AC: 1060 AN: 10410

Middle Eastern (MID) AF: 0.143 AC: 42 AN: 294

European-Non Finnish (NFE) AF: 0.0990 AC: 6728 AN: 67934

Other (OTH) AF: 0.0868 AC: 183 AN: 2108

Alfa AF: 0.0967 Hom.: 414

Bravo AF: 0.0881

Asia WGS AF: 0.118 AC: 409 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	1.3
DANN	Benign	0.51
PhyloP100		-0.58

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: rs10499196;

hg19: chr6-138019666;