chr4-103580381-C-A

Variant names:

• chr4-103580381-C-A
• rs2868397
• ENST00000502936.1:n.190-10826C>A

Variant summary

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

The ENST00000502936.1(TACR3-AS1):​n.190-10826C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0504 in 152,286 control chromosomes in the GnomAD database, including 431 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 0.050 (431 hom., cov: 32)
• Consequence: TACR3-AS1 ENST00000502936.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.592
• Publications: 2 publications found

Genes affected

TACR3-AS1 (HGNC:55593): (TACR3 antisense RNA 1)

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 (EAS) allele frequency at 95% confidence interval = 0.234 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TACR3-AS1	NR_186501.1	n.190-10826C>A		intron_variant	Intron 2 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TACR3-AS1	ENST00000502936.1	n.190-10826C>A		intron_variant	Intron 2 of 4	2
TACR3-AS1	ENST00000512401.5	n.292-10826C>A		intron_variant	Intron 3 of 4	2

Frequencies

GnomAD3 genomes AF: 0.0504 AC: 7664 AN: 152168 Hom.: 428 Cov.: 32

Gnomad AFR AF: 0.00878

Gnomad AMI AF: 0.00329

Gnomad AMR AF: 0.0697

Gnomad ASJ AF: 0.0475

Gnomad EAS AF: 0.245

Gnomad SAS AF: 0.216

Gnomad FIN AF: 0.0551

Gnomad MID AF: 0.108

Gnomad NFE AF: 0.0445

Gnomad OTH AF: 0.0516

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

GnomAD4 genome AF: 0.0504 AC: 7669 AN: 152286 Hom.: 431 Cov.: 32 AF XY: 0.0564 AC XY: 4196 AN XY: 74458

African (AFR) AF: 0.00876 AC: 364 AN: 41562

American (AMR) AF: 0.0700 AC: 1070 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.0475 AC: 165 AN: 3472

East Asian (EAS) AF: 0.245 AC: 1269 AN: 5174

South Asian (SAS) AF: 0.217 AC: 1045 AN: 4820

European-Finnish (FIN) AF: 0.0551 AC: 585 AN: 10614

Middle Eastern (MID) AF: 0.105 AC: 31 AN: 294

European-Non Finnish (NFE) AF: 0.0445 AC: 3025 AN: 68028

Other (OTH) AF: 0.0530 AC: 112 AN: 2114

Alfa AF: 0.0458 Hom.: 276

Bravo AF: 0.0469

Asia WGS AF: 0.197 AC: 682 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	0.48
DANN	Benign	0.66
PhyloP100		-0.59
Mutation Taster		=100/0	polymorphism

Splicing

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

Other links and lift over

dbSNP: rs2868397; hg19: chr4-104501538;