XR_001751636.2:n.4836T>C

Variant names:

• chr15-81643694-A-G
• rs718276
• XR_001751636.2:n.4836T>C

Variant summary

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

The XR_001751636.2(LOC102723985):​n.4836T>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 0.323 in 151,988 control chromosomes in the GnomAD database, including 9,497 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 0.32 (9497 hom., cov: 32)
• Consequence: LOC102723985 XR_001751636.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0840
• Publications: 3 publications found

Genes affected

LOC102723985 (HGNC:):

TMC3-AS1 (HGNC:51424): (TMC3 antisense RNA 1)

LINC01418 (HGNC:50711): (long intergenic non-protein coding RNA 1418)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.623 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC102723985	XR_001751636.2	n.4836T>C		non_coding_transcript_exon_variant	Exon 3 of 4
LOC102723985	XR_007064735.1	n.19108T>C		non_coding_transcript_exon_variant	Exon 3 of 4
LOC102723985	XR_007064738.1	n.20079T>C		non_coding_transcript_exon_variant	Exon 2 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TMC3-AS1	ENST00000558141.5	n.29-24474A>G		intron_variant	Intron 1 of 2	3
ENSG00000259543	ENST00000559211.1	n.266+33518A>G		intron_variant	Intron 2 of 3	4
LINC01418	ENST00000559428.2	n.96-1259T>C		intron_variant	Intron 1 of 2	3

Frequencies

GnomAD3 genomes AF: 0.322 AC: 48969 AN: 151870 Hom.: 9478 Cov.: 32

Gnomad AFR AF: 0.489

Gnomad AMI AF: 0.184

Gnomad AMR AF: 0.426

Gnomad ASJ AF: 0.266

Gnomad EAS AF: 0.641

Gnomad SAS AF: 0.235

Gnomad FIN AF: 0.161

Gnomad MID AF: 0.241

Gnomad NFE AF: 0.211

Gnomad OTH AF: 0.319

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

GnomAD4 genome AF: 0.323 AC: 49044 AN: 151988 Hom.: 9497 Cov.: 32 AF XY: 0.323 AC XY: 24024 AN XY: 74282

African (AFR) AF: 0.489 AC: 20232 AN: 41408

American (AMR) AF: 0.427 AC: 6520 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.266 AC: 924 AN: 3470

East Asian (EAS) AF: 0.641 AC: 3304 AN: 5154

South Asian (SAS) AF: 0.236 AC: 1135 AN: 4818

European-Finnish (FIN) AF: 0.161 AC: 1706 AN: 10584

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

European-Non Finnish (NFE) AF: 0.211 AC: 14312 AN: 67956

Other (OTH) AF: 0.318 AC: 670 AN: 2108

Alfa AF: 0.281 Hom.: 1160

Bravo AF: 0.357

Asia WGS AF: 0.404 AC: 1405 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	1.4
DANN	Benign	0.83
PhyloP100		-0.084

Splicing

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

Other links and lift over

dbSNP: rs718276; hg19: chr15-81936035;